[BioC] error in loading affy (R 2.0), Thank you
Pintilie, Melania
Melania.Pintilie at uhn.on.ca
Fri Oct 29 16:34:23 CEST 2004
Hi everyone,
I would like to thank
Zhao, Xiaohong (NIH/NCI) [zhaoxiao at mail.nih.gov]
Tarca Adi Laurentiu [ltarca at rsvs.ulaval.ca]
James MacDonald" <jmacdon at med.umich.edu>
who gave me valuable suggestions.
Based on these I did the following and it worked:
> source("http://www.bioconductor.org/getBioC.R")
> getBioC(develOK=TRUE)
> install.packages2("affy",develOK=T)
Melania
Rm 15-433, ext 4886
Fax: (416) 946-2048
-----Original Message-----
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Sent: Thursday, October 28, 2004 6:07 AM
To: bioconductor at stat.math.ethz.ch
Subject: Bioconductor Digest, Vol 20, Issue 27
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Today's Topics:
1. GeneExpressionOmnibus (GEO) question (Ilya Venger)
2. normalization with large amount of significant genes (Ana Conesa)
3. Combining MOE430A and MOE4302 (Scott Ochsner)
4. error readAffy (Auer Michael)
5. Loading package multtest (Prof. Dr. L. Hothorn)
6. reposTools: problem with download.packages2 (Matthias Burger)
7. Re: reposTools: problem with download.packages2 (Jeff Gentry)
8. How can I put color scale & legend on Heatmap (Saurin Jani)
9. Re: Combining MOE430A and MOE4302 (Wolfgang Huber)
10. Problem installing graph package (Matt McCall)
11. Re: Problem installing graph package (Robert Gentleman)
12. globaltest : geneplot & sample plot (Saurin Jani)
13. Missing GO terms in GOLOCUSID2GO (jeffrey rasmussen)
14. Re: Missing GO terms in GOLOCUSID2GO (Robert Gentleman)
15. Re: Problem installing graph package (Byron Ellis)
16. Re: Color in the lefs of a dendrogram? (Martin Maechler)
17. Comparison of Affymetrix and CodeLink chip (Binita Dutta)
----------------------------------------------------------------------
Message: 1
Date: Wed, 27 Oct 2004 13:33:36 +0200
From: Ilya Venger <ilya.venger at weizmann.ac.il>
Subject: [BioC] GeneExpressionOmnibus (GEO) question
To: bioconductor at stat.math.ethz.ch
Message-ID: <417F8790.3040100 at weizmann.ac.il>
Content-Type: text/plain; charset=us-ascii; format=flowed
I know that I can query the GEO database using the AnnBuilder package.
However, I don't know exactly what to do next.
NCBI states that the data they present in GDS accessions is normalized,
but they don't explain how.
The GSMs of different contributors not necessarily match, and they
sometimes lack parts of the data. Also, if the raw data is submitted,
how come they don't show the measurements for both repetitions of each
gene in a cDNA array.
Another problem, is that although the GDS are claimed to be normalized
the sum of logs for all genes on a chip doesn't sum to 0.
So, if anybody worked with GEO before, and has experience at it I would
be glad to pose several more specific questions.
------------------------------
Message: 2
Date: Wed, 27 Oct 2004 15:47:53 +0200
From: Ana Conesa <aconesa at ivia.es>
Subject: [BioC] normalization with large amount of significant genes
To: bioconductor at stat.math.ethz.ch
Message-ID: <6.1.0.6.0.20041027132513.01c5ee00 at master.ivia.es>
Content-Type: text/plain; charset="iso-8859-1"
------------------------------
Message: 3
Date: Wed, 27 Oct 2004 09:15:59 -0500
From: "Scott Ochsner" <sochsner at bcm.tmc.edu>
Subject: [BioC] Combining MOE430A and MOE4302
To: "'Bioconductor'" <bioconductor at stat.math.ethz.ch>
Message-ID: <200410271416.JAA15363 at bran.bcm.tmc.edu>
Content-Type: text/plain
I have two sets of CEL files: one from MOE430A and one from MOE4302. I
would like to normalize similar probe sets across the chip types but I am
unable to combine Affybatches as they are different sizes. This was touched
on previously in this list serve concerning the combination of HGU133A and
HGU133 Plus2.0 chips. I could not, however, find an answer to the problem
in this thread.
I was thinking I could restructure the existing MOE4302 affybatch by
subtracting/removing the MOE430B probe set data and then proceed to
combining this with the existing MOE430A affybatch. I am able to perform
routine R manipulations but the subtracting scheme detailed above is beyond
my scope.
Scott Ochsner, Ph.D.
Huffington Center on Aging, M810
Baylor College of Medicine
Houston, TX. 77030
Lab: 713-798-1620
Office: 713-798-1585
[[alternative HTML version deleted]]
------------------------------
Message: 4
Date: Wed, 27 Oct 2004 16:23:25 +0200 (CEST)
From: "Auer Michael" <michael.auer at meduniwien.ac.at>
Subject: [BioC] error readAffy
To: bioconductor at stat.math.ethz.ch
Message-ID: <1284.80.108.125.179.1098887005.squirrel at 80.108.125.179>
Content-Type: text/plain;charset=iso-8859-1
I am using Windows XP, R 2.0.0. and affy package 1.5.8
I have copied the files to the folder "//Marvel-xms4rmgc/festplatte/A2M
Lab/01 Customers/AKH/Erowic/data/filename.cel"
sample.names<- c("SCC9_A_0"," SCC9_A_C"," SCC9_A_N"," SCC9_A_CN",
"SCC9_B_0"," SCC9_B_C"," SCC9_B_N"," SCC9_B_CN", "SCC9_C_0"," SCC9_C_C","
SCC9_C_N"," SCC9_C_CN")
sample.files<-c("//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 A o.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 A c.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC9 A n.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 A c+n.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B o.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B c.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B n.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B c+n.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102204_sample SSC9 C o.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102204_sample SSC9 C c.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102204_sample SSC9 C n.CEL",
"//Marvel-xms4rmgc/festplatte/A2M Lab/01
Customers/AKH/Erowic/data/BE_102204_sample SSC9 C c+n.CEL")
I am loading the library
library(affy)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: reposTools
Then I am using ReadAffy and the following error message occurs with two
of the arrays.
pleca<-ReadAffy(filenames=sample.files,sampleNames =sample.names)
Error in initialize(value, ...) : Could not open file //Marvel-xm
4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102204_sample
SSC9 C n.CEL
What is the problem? Can anybody help. I can't go back to a former
release, because R 2.0.0. doesn't accept it.
Thanks
------------------------------
Message: 5
Date: Wed, 27 Oct 2004 08:58:57 +0200
From: "Prof. Dr. L. Hothorn" <hothorn at bioinf.uni-hannover.de>
Subject: [BioC] Loading package multtest
To: bioconductor at stat.math.ethz.ch
Message-ID:
<6.0.0.22.0.20041027085714.01c15e60 at mail.bioinf.uni-hannover.de>
Content-Type: text/plain; charset="us-ascii"
------------------------------
Message: 6
Date: Wed, 27 Oct 2004 12:24:52 +0200
From: Matthias Burger <matthias.burger at epigenomics.com>
Subject: [BioC] reposTools: problem with download.packages2
To: bioconductor at stat.math.ethz.ch
Message-ID: <417F7774.3090404 at epigenomics.com>
Content-Type: text/plain; charset=us-ascii; format=flowed
Hi,
i used the following calls to download all of Windows packages stored
on the BioC CRAN mirror, but the executions tops with an error report on
a package (CoCo) only available as source pkg.
Did I make a mistake, or misunderstand the docu? I had thought the type
argument would take care of this?
Thanks for any adivse how to get this working.
Regards,
Matthias
z <- repositories()
## select: 1
ok <- download.packages2(repEntry=z,
destDir="/mnt/local/R/windows/R-contrib/contrib-2.0.0/CRAN/", type="Win32")
...
[1] "Attempting to download CoCoAn from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
Error in download.packages2(repEntry = z, destDir =
"/mnt/local/R/windows/R-contrib/contrib-2.0.0/CRAN/", :
Package CoCo is not available at
http://www.bioconductor.org//CRANrepository
details:
reposTools 1.4.13
>version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 0.0
year 2004
month 10
day 04
language R
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AG Kleine Praesidentenstr. 1 10178 Berlin, Germany
phone:+49-30-24345-371 fax:+49-30-24345-555
http://www.epigenomics.com matthias.burger at epigenomics.com
------------------------------
Message: 7
Date: Wed, 27 Oct 2004 10:35:40 -0400 (EDT)
From: Jeff Gentry <jgentry at jimmy.harvard.edu>
Subject: Re: [BioC] reposTools: problem with download.packages2
To: Matthias Burger <matthias.burger at epigenomics.com>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.SOL.4.20.0410271035000.18197-100000 at santiam.dfci.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> i used the following calls to download all of Windows packages stored
> on the BioC CRAN mirror, but the executions tops with an error report on
> a package (CoCo) only available as source pkg.
Well, it is only avail as a source package. :)
Did the execution halt right there, or did it get all of the packages and
just say that it couldn't get CoCo at the end? Not sure exactly which
you're describing here.
------------------------------
Message: 8
Date: Wed, 27 Oct 2004 08:42:10 -0700 (PDT)
From: Saurin Jani <saurin_jani at yahoo.com>
Subject: [BioC] How can I put color scale & legend on Heatmap
To: Bioconductor Bioconductor <bioconductor at stat.math.ethz.ch>
Message-ID: <20041027154210.65125.qmail at web41124.mail.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Hi,
On my heatmap, I am doing:
> rbg <- maPalette(low="blue", high="red",
mid="white")
> Feature_GeneNames <- mget(unique(myFeatureGenes),env
= moe430aGENENAME);
> row.names(esetFeatureX) <- Feature_GeneNames;
> colnames(esetFeatureX) <- samples;
> heatmap(esetFeatureX,Rowv= NA ,Colv=
NA,col=rbg,margins=c(10,30));
I can see nice heat map, but how should I put legend
on heatmap image because legend() does seem to work in
combination of heatmap. May be I am doing something
wrong.
How can I put legend & color scale below heatmap
image.
Any heatmap suggestion would be great..!
Thank you,
Saurin
------------------------------
Message: 9
Date: Wed, 27 Oct 2004 19:47:40 +0100
From: Wolfgang Huber <huber at ebi.ac.uk>
Subject: Re: [BioC] Combining MOE430A and MOE4302
To: bioconductor at stat.math.ethz.ch
Message-ID: <417FED4C.9080302 at ebi.ac.uk>
Content-Type: text/plain; charset=us-ascii; format=flowed
Scott Ochsner wrote:
> I have two sets of CEL files: one from MOE430A and one from MOE4302. I
> would like to normalize similar probe sets across the chip types but I am
> unable to combine Affybatches as they are different sizes. This was
touched
> on previously in this list serve concerning the combination of HGU133A and
> HGU133 Plus2.0 chips. I could not, however, find an answer to the problem
> in this thread.
Can you be more be more specific about "unable to combine Affybatches as
they are different sizes"? Did you try the function combineAffyBatcg
from package matchprobes?
Bw
Wolfgang
--
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http: www.dkfz.de/abt0840/whuber
------------------------------
Message: 10
Date: Wed, 27 Oct 2004 14:28:50 -0400
From: Matt McCall <mmccall at mail.nih.gov>
Subject: [BioC] Problem installing graph package
To: bioconductor at stat.math.ethz.ch
Message-ID: <0CB2F3EB-2846-11D9-B275-000A95AFE190 at mail.nih.gov>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Using R v2.0.0 on MacOS X in the R console.
I was able to install most of bioconductor. I wanted to use the GOstats
package (amoung a few others), and it didn't install properly. So I
went back to try to find the problem, and it seems that the graph
package isn't installing. Any suggestions?
Matt
> getBioC("prog", develOK=T)
Running getBioC version 1.2.66....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
Please direct any concerns or questions to
bioconductor at stat.math.ethz.ch.
Please select an installation directory:
1:/Users/mmccall/Library/R/library
2:/Library/Frameworks/R.framework/Resources/library
Selection: 1
[1] "Attempting to download graph from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing graph"
* Installing *source* package 'graph' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o
graph.c: In function `intersectStrings':
graph.c:39: warning: assignment makes pointer from integer without a
cast
graph.c:56: warning: assignment makes pointer from integer without a
cast
graph.c: In function `graphIntersection':
graph.c:118: warning: assignment makes pointer from integer without a
cast
graph.c: In function `checkEdgeList':
graph.c:157: warning: assignment makes pointer from integer without a
cast
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
graph.so graph.o -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** save image
[1] TRUE
[1] TRUE
[1] TRUE
Loading required package: cluster
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
[1] "propertyHolder"
[1] "property"
[1] "property"
[1] "property<-"
[1] "property<-"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "graph"
[1] "edgemode"
[1] "edgemode"
[1] "edgemode<-"
[1] "edgemode<-"
[1] "graphNEL"
[1] "initialize"
[1] "nodes"
[1] "nodes"
[1] "nodes<-"
[1] "nodes<-"
[1] "edges"
[1] "edges"
[1] "edges"
[1] "degree"
[1] "degree"
[1] "degree"
[1] "edgeWeights"
[1] "edgeWeights"
[1] "adj"
[1] "adj"
[1] "acc"
[1] "acc"
[1] "DFS"
[1] "DFS"
[1] "edgeL"
[1] "edgeL"
[1] "subGraph"
[1] "subGraph"
[1] "intersection2"
[1] "intersection2"
[1] "intersection"
[1] "intersection"
[1] "join"
[1] "join"
[1] "union"
[1] "union"
[1] "complement"
[1] "complement"
[1] "connComp"
[1] "connComp"
[1] "isConnected"
[1] "isConnected"
[1] "numNodes"
[1] "numNodes"
[1] "numNodes"
[1] "addNode"
[1] "addNode"
[1] "addNode"
[1] "removeNode"
[1] "removeNode"
[1] "clearNode"
[1] "clearNode"
[1] "removeEdge"
[1] "removeEdge"
[1] "addEdge"
[1] "addEdge"
[1] "combineNodes"
[1] "combineNodes"
[1] "inEdges"
[1] "inEdges"
[1] "inEdges"
[1] "inEdges"
[1] "show"
[1] "edgeNames"
[1] "edgeNames"
[1] "clusteringCoefficient"
[1] "clusteringCoefficient"
Error in assign("nullgraphID", getuuid()) :
couldn't find function "getuuid"
Execution halted
cat: ** Removing '/Users/mmccall/Library/R/library/graph'
** Restoring previous '/Users/mmccall/Library/R/library/graph'
stdout: Broken pipe
ERROR: execution of package source for 'graph' failed
[1] "Attempting to download hexbin from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing hexbin"
* Installing *source* package 'hexbin' ...
** libs
g77 -fno-common -g -O2 -c hbin.f -o hbin.o
** Removing '/Users/mmccall/Library/R/library/hexbin'
make: g77: Command not found
make: *** [hbin.o] Error 127
ERROR: compilation failed for package 'hexbin'
** Restoring previous '/Users/mmccall/Library/R/library/hexbin'
[1] "Attempting to download Ruuid from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing Ruuid"
* Installing *source* package 'Ruuid' ...
creating cache ./config.cache
checking for glib-config... no
checking how to run the C preprocessor... cc -E
checking for /usr/include/unistd.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include
-fno-common -g -O2 -c Rinit.c -o Rinit.o
In file included from Ruuid.h:5,
from Rinit.c:1:
uuidP.h:24:18: glib.h: No such file or directory
In file included from Ruuid.h:5,
from Rinit.c:1:
uuidP.h:36: error: parse error before "guint32"
uuidP.h:36: warning: no semicolon at end of struct or union
uuidP.h:37: warning: data definition has no type or storage class
uuidP.h:38: error: parse error before "time_hi_and_version"
uuidP.h:38: warning: data definition has no type or storage class
uuidP.h:39: error: parse error before "clock_seq"
uuidP.h:39: warning: data definition has no type or storage class
uuidP.h:40: error: parse error before "node"
uuidP.h:40: warning: data definition has no type or storage class
uuidP.h:41: error: parse error before '}' token
** Removing '/Users/mmccall/Library/R/library/Ruuid'
** Restoring previous '/Users/mmccall/Library/R/library/Ruuid'
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package 'Ruuid'
From URL: http://www.bioconductor.org/repository/devel/package/Source
graph version 1.4.22
hexbin version 1.1-2
Ruuid version 1.4.5
Packages Rgraphviz and rhdf5 require special libraries to be installed.
Please see the URL http://www.bioconductor.org/faq.html#Other Notes for
more details on installing these packages if they fail
to install properly
Warning messages:
1: Installation of package graph had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
2: Installation of package hexbin had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
3: Installation of package Ruuid had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
>
------------------------------
Message: 11
Date: Wed, 27 Oct 2004 14:44:41 -0400
From: Robert Gentleman <rgentlem at jimmy.harvard.edu>
Subject: Re: [BioC] Problem installing graph package
To: Matt McCall <mmccall at mail.nih.gov>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <20041027144441.A5500 at jimmy.harvard.edu>
Content-Type: text/plain; charset=us-ascii
Hi,
First your real problem is that you do not have Ruuid installed (and
that is what graph reports as the problem). So that would be your
first port of call. There are some details of how to do this, and
what libraries you need in the mailing list archives.
so do install.packages2("Ruuid")
and then see what libraries you do not have installed on your system,
then get them and install them.
Second, you do not have g77, so you won't be able to install any
fortran code (and that is what is in hexbin). Again, this is because
you lack the right tools in OS X, so you need to find them and
install them. Stefano Iacus keeps a nice web page that describes what
you need to have installed etc. for building R packages. The OS X
FAQ, is another place to look for details (and probably the first
place to look),
Best
Robert
On Wed, Oct 27, 2004 at 02:28:50PM -0400, Matt McCall wrote:
> Using R v2.0.0 on MacOS X in the R console.
> I was able to install most of bioconductor. I wanted to use the GOstats
> package (amoung a few others), and it didn't install properly. So I
> went back to try to find the problem, and it seems that the graph
> package isn't installing. Any suggestions?
> Matt
>
> > getBioC("prog", develOK=T)
> Running getBioC version 1.2.66....
> If you encounter problems, first make sure that
> you are running the latest version of getBioC()
> which can be found at: www.bioconductor.org/getBioC.R
>
> Please direct any concerns or questions to
> bioconductor at stat.math.ethz.ch.
>
> Please select an installation directory:
> 1:/Users/mmccall/Library/R/library
> 2:/Library/Frameworks/R.framework/Resources/library
> Selection: 1
> [1] "Attempting to download graph from
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing graph"
> * Installing *source* package 'graph' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o
> graph.c: In function `intersectStrings':
> graph.c:39: warning: assignment makes pointer from integer without a
> cast
> graph.c:56: warning: assignment makes pointer from integer without a
> cast
> graph.c: In function `graphIntersection':
> graph.c:118: warning: assignment makes pointer from integer without a
> cast
> graph.c: In function `checkEdgeList':
> graph.c:157: warning: assignment makes pointer from integer without a
> cast
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
> graph.so graph.o -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> [1] TRUE
> [1] TRUE
> Loading required package: cluster
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> Vignettes contain introductory material. To view,
> simply type: openVignette()
> For details on reading vignettes, see
> the openVignette help page.
> [1] "propertyHolder"
> [1] "property"
> [1] "property"
> [1] "property<-"
> [1] "property<-"
> [1] "asGraphProperty"
> [1] "asGraphProperty"
> [1] "asGraphProperty"
> [1] "asGraphProperty"
> [1] "asGraphProperty"
> [1] "graph"
> [1] "edgemode"
> [1] "edgemode"
> [1] "edgemode<-"
> [1] "edgemode<-"
> [1] "graphNEL"
> [1] "initialize"
> [1] "nodes"
> [1] "nodes"
> [1] "nodes<-"
> [1] "nodes<-"
> [1] "edges"
> [1] "edges"
> [1] "edges"
> [1] "degree"
> [1] "degree"
> [1] "degree"
> [1] "edgeWeights"
> [1] "edgeWeights"
> [1] "adj"
> [1] "adj"
> [1] "acc"
> [1] "acc"
> [1] "DFS"
> [1] "DFS"
> [1] "edgeL"
> [1] "edgeL"
> [1] "subGraph"
> [1] "subGraph"
> [1] "intersection2"
> [1] "intersection2"
> [1] "intersection"
> [1] "intersection"
> [1] "join"
> [1] "join"
> [1] "union"
> [1] "union"
> [1] "complement"
> [1] "complement"
> [1] "connComp"
> [1] "connComp"
> [1] "isConnected"
> [1] "isConnected"
> [1] "numNodes"
> [1] "numNodes"
> [1] "numNodes"
> [1] "addNode"
> [1] "addNode"
> [1] "addNode"
> [1] "removeNode"
> [1] "removeNode"
> [1] "clearNode"
> [1] "clearNode"
> [1] "removeEdge"
> [1] "removeEdge"
> [1] "addEdge"
> [1] "addEdge"
> [1] "combineNodes"
> [1] "combineNodes"
> [1] "inEdges"
> [1] "inEdges"
> [1] "inEdges"
> [1] "inEdges"
> [1] "show"
> [1] "edgeNames"
> [1] "edgeNames"
> [1] "clusteringCoefficient"
> [1] "clusteringCoefficient"
> Error in assign("nullgraphID", getuuid()) :
> couldn't find function "getuuid"
> Execution halted
> cat: ** Removing '/Users/mmccall/Library/R/library/graph'
> ** Restoring previous '/Users/mmccall/Library/R/library/graph'
> stdout: Broken pipe
> ERROR: execution of package source for 'graph' failed
> [1] "Attempting to download hexbin from
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing hexbin"
> * Installing *source* package 'hexbin' ...
> ** libs
> g77 -fno-common -g -O2 -c hbin.f -o hbin.o
> ** Removing '/Users/mmccall/Library/R/library/hexbin'
> make: g77: Command not found
> make: *** [hbin.o] Error 127
> ERROR: compilation failed for package 'hexbin'
> ** Restoring previous '/Users/mmccall/Library/R/library/hexbin'
> [1] "Attempting to download Ruuid from
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing Ruuid"
> * Installing *source* package 'Ruuid' ...
> creating cache ./config.cache
> checking for glib-config... no
> checking how to run the C preprocessor... cc -E
> checking for /usr/include/unistd.h... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include
> -fno-common -g -O2 -c Rinit.c -o Rinit.o
> In file included from Ruuid.h:5,
> from Rinit.c:1:
> uuidP.h:24:18: glib.h: No such file or directory
> In file included from Ruuid.h:5,
> from Rinit.c:1:
> uuidP.h:36: error: parse error before "guint32"
> uuidP.h:36: warning: no semicolon at end of struct or union
> uuidP.h:37: warning: data definition has no type or storage class
> uuidP.h:38: error: parse error before "time_hi_and_version"
> uuidP.h:38: warning: data definition has no type or storage class
> uuidP.h:39: error: parse error before "clock_seq"
> uuidP.h:39: warning: data definition has no type or storage class
> uuidP.h:40: error: parse error before "node"
> uuidP.h:40: warning: data definition has no type or storage class
> uuidP.h:41: error: parse error before '}' token
> ** Removing '/Users/mmccall/Library/R/library/Ruuid'
> ** Restoring previous '/Users/mmccall/Library/R/library/Ruuid'
> make: *** [Rinit.o] Error 1
> ERROR: compilation failed for package 'Ruuid'
> From URL: http://www.bioconductor.org/repository/devel/package/Source
> graph version 1.4.22
> hexbin version 1.1-2
> Ruuid version 1.4.5
>
> Packages Rgraphviz and rhdf5 require special libraries to be installed.
> Please see the URL http://www.bioconductor.org/faq.html#Other Notes for
> more details on installing these packages if they fail
> to install properly
>
> Warning messages:
> 1: Installation of package graph had non-zero exit status in:
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> 2: Installation of package hexbin had non-zero exit status in:
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> 3: Installation of package Ruuid had non-zero exit status in:
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
+---------------------------------------------------------------------------
+
| Robert Gentleman phone : (617) 632-5250
|
| Associate Professor fax: (617) 632-2444
|
| Department of Biostatistics office: M1B20
|
| Harvard School of Public Health email: rgentlem at jimmy.harvard.edu
|
+---------------------------------------------------------------------------
+
------------------------------
Message: 12
Date: Wed, 27 Oct 2004 12:22:22 -0700 (PDT)
From: Saurin Jani <saurin_jani at yahoo.com>
Subject: [BioC] globaltest : geneplot & sample plot
To: Bioconductor Bioconductor <bioconductor at stat.math.ethz.ch>
Message-ID: <20041027192222.38645.qmail at web41112.mail.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Hi,
> path1 <- kegg[["00280"]];
> globaltest_all <-
globaltest(esetSub2,pData(esetSub2)[,"scanner2"],test.genes
= path1,model = "logistic");
> geneplot(globaltest_all,labelsize = 1);
here, it shows only 1 gene(145512_at) out of my all 6
samples. I have 3 Knock Out and 3 Wild Type samples.
> sampleplot(globaltest_all,labelsize = 1);
here, I can see all 6 sample plots look similar ,
Knock out and Wild Type. Very less difference.
I think , it should only show Knock out sample at
higher bar..right..!
Am I doing something wrong or I have wrong
undertanding..about sampleplot and geneplots. (or Need
to read more about that)
Please let me know..if anyone..!
Thanks,
Saurin
------------------------------
Message: 13
Date: Wed, 27 Oct 2004 13:36:18 -0700 (PDT)
From: jeffrey rasmussen <rasmuss at u.washington.edu>
Subject: [BioC] Missing GO terms in GOLOCUSID2GO
To: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.A41.4.61b.0410271322460.264822 at homer11.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Using GO 1.6.5 the following code produces a list of GO terms that are
annotated as being connected with a certain LL id, but have their
"Ontology" slot listed as "NA" (presumably because they are missing from
GOTERM and the other GO* objects):
library(GO)
ll2go <- as.list.environment(GOLOCUSID2GO)
tmp <- lapply(ll2go, function (x) sapply(x, function(x)
if(is.na(x$Ontology)){ print(x$GOID) }))
Perhaps a more recent file was used to build GOLOCUSID2GO than was used to
build the remaining GO annotations?
Jeff.
(Here's the list of missing terms)
GO:0001880
GO:0001881
GO:0001883
GO:0001886
GO:0030968
GO:0030970
GO:0030971
GO:0035199
GO:0035211
GO:0035214
GO:0035215
GO:0035224
GO:0035226
GO:0035227
GO:0035229
GO:0035232
GO:0035233
GO:0035234
GO:0043185
GO:0043190
GO:0043197
GO:0043198
GO:0048488
GO:0048489
GO:0051082
GO:0051087
GO:0051089
GO:0051092
GO:0051097
GO:0051101
GO:0051106
------------------------------
Message: 14
Date: Wed, 27 Oct 2004 16:41:49 -0400
From: Robert Gentleman <rgentlem at jimmy.harvard.edu>
Subject: Re: [BioC] Missing GO terms in GOLOCUSID2GO
To: jeffrey rasmussen <rasmuss at u.washington.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <20041027164149.H5500 at jimmy.harvard.edu>
Content-Type: text/plain; charset=us-ascii
Funny you should ask...
yes we just noticed this. It seems to be a problem somewhere in the
data we obtained. It is most likely that we will drop these - they
can often be hand curated, but hands are the one thing we are very
short of...so anyone looking for something constructive to do...we
have lots of basic mundane things (on which more excting and less
mundane things can be built) that are not getting done.
Robert
On Wed, Oct 27, 2004 at 01:36:18PM -0700, jeffrey rasmussen wrote:
> Using GO 1.6.5 the following code produces a list of GO terms that are
> annotated as being connected with a certain LL id, but have their
> "Ontology" slot listed as "NA" (presumably because they are missing from
> GOTERM and the other GO* objects):
>
> library(GO)
> ll2go <- as.list.environment(GOLOCUSID2GO)
> tmp <- lapply(ll2go, function (x) sapply(x, function(x)
> if(is.na(x$Ontology)){ print(x$GOID) }))
>
> Perhaps a more recent file was used to build GOLOCUSID2GO than was used to
> build the remaining GO annotations?
>
> Jeff.
>
> (Here's the list of missing terms)
>
> GO:0001880
> GO:0001881
> GO:0001883
> GO:0001886
> GO:0030968
> GO:0030970
> GO:0030971
> GO:0035199
> GO:0035211
> GO:0035214
> GO:0035215
> GO:0035224
> GO:0035226
> GO:0035227
> GO:0035229
> GO:0035232
> GO:0035233
> GO:0035234
> GO:0043185
> GO:0043190
> GO:0043197
> GO:0043198
> GO:0048488
> GO:0048489
> GO:0051082
> GO:0051087
> GO:0051089
> GO:0051092
> GO:0051097
> GO:0051101
> GO:0051106
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
+---------------------------------------------------------------------------
+
| Robert Gentleman phone : (617) 632-5250
|
| Associate Professor fax: (617) 632-2444
|
| Department of Biostatistics office: M1B20
|
| Harvard School of Public Health email: rgentlem at jimmy.harvard.edu
|
+---------------------------------------------------------------------------
+
------------------------------
Message: 15
Date: Thu, 28 Oct 2004 00:05:27 -0700
From: Byron Ellis <bellis at hsph.harvard.edu>
Subject: Re: [BioC] Problem installing graph package
To: Robert Gentleman <rgentlem at jimmy.harvard.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <BF340E92-28AF-11D9-B678-000D93C24D64 at hsph.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Subscribing to the Mac SIG mailing list might also be a good idea, it
can be really useful when g77 goes weird on you.
Oh, and the repository version of Ruuid doesn't require glib on OS X
(sort of a heavy requirement for something like 5 typedefs), you might
try building that version instead.
On Oct 27, 2004, at 11:44 AM, Robert Gentleman wrote:
> Hi,
> First your real problem is that you do not have Ruuid installed (and
> that is what graph reports as the problem). So that would be your
> first port of call. There are some details of how to do this, and
> what libraries you need in the mailing list archives.
>
> so do install.packages2("Ruuid")
> and then see what libraries you do not have installed on your system,
> then get them and install them.
>
> Second, you do not have g77, so you won't be able to install any
> fortran code (and that is what is in hexbin). Again, this is because
> you lack the right tools in OS X, so you need to find them and
> install them. Stefano Iacus keeps a nice web page that describes what
> you need to have installed etc. for building R packages. The OS X
> FAQ, is another place to look for details (and probably the first
> place to look),
>
> Best
> Robert
>
> On Wed, Oct 27, 2004 at 02:28:50PM -0400, Matt McCall wrote:
>> Using R v2.0.0 on MacOS X in the R console.
>> I was able to install most of bioconductor. I wanted to use the
>> GOstats
>> package (amoung a few others), and it didn't install properly. So I
>> went back to try to find the problem, and it seems that the graph
>> package isn't installing. Any suggestions?
>> Matt
>>
>>> getBioC("prog", develOK=T)
>> Running getBioC version 1.2.66....
>> If you encounter problems, first make sure that
>> you are running the latest version of getBioC()
>> which can be found at: www.bioconductor.org/getBioC.R
>>
>> Please direct any concerns or questions to
>> bioconductor at stat.math.ethz.ch.
>>
>> Please select an installation directory:
>> 1:/Users/mmccall/Library/R/library
>> 2:/Library/Frameworks/R.framework/Resources/library
>> Selection: 1
>> [1] "Attempting to download graph from
>> http://www.bioconductor.org/repository/devel/package/Source"
>> [1] "Download complete."
>> [1] "Installing graph"
>> * Installing *source* package 'graph' ...
>> ** libs
>> gcc -no-cpp-precomp
>> -I/Library/Frameworks/R.framework/Resources/include
>> -I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o
>> graph.c: In function `intersectStrings':
>> graph.c:39: warning: assignment makes pointer from integer without a
>> cast
>> graph.c:56: warning: assignment makes pointer from integer without a
>> cast
>> graph.c: In function `graphIntersection':
>> graph.c:118: warning: assignment makes pointer from integer without a
>> cast
>> graph.c: In function `checkEdgeList':
>> graph.c:157: warning: assignment makes pointer from integer without a
>> cast
>> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
>> graph.so graph.o -lcc_dynamic -framework R
>> ld: warning multiple definitions of symbol _xerbla_
>> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
>> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
>> _xerbla_
>> ld: warning multiple definitions of symbol _crc32
>> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
>> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
>> ld: warning multiple definitions of symbol _get_crc_table
>> /Library/Frameworks/R.framework/R(crc32.lo) definition of
>> _get_crc_table
>> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
>> ld: warning multiple definitions of symbol _deflate
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
>> ld: warning multiple definitions of symbol _deflateCopy
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateCopy
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
>> ld: warning multiple definitions of symbol _deflateReset
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateReset
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
>> ld: warning multiple definitions of symbol _deflateSetDictionary
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateSetDictionary
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
>> ld: warning multiple definitions of symbol _deflateInit2_
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateInit2_
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
>> ld: warning multiple definitions of symbol _deflateEnd
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateEnd
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
>> ld: warning multiple definitions of symbol _deflateParams
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateParams
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
>> ld: warning multiple definitions of symbol _deflateInit_
>> /Library/Frameworks/R.framework/R(deflate.lo) definition of
>> _deflateInit_
>> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
>> ld: warning multiple definitions of symbol _zError
>> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
>> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
>> ld: warning multiple definitions of symbol _zlibVersion
>> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
>> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
>> ld: warning multiple definitions of symbol _inflateEnd
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateEnd
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
>> ld: warning multiple definitions of symbol _inflateSync
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateSync
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
>> ld: warning multiple definitions of symbol _inflateSyncPoint
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateSyncPoint
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
>> ld: warning multiple definitions of symbol _inflate
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
>> ld: warning multiple definitions of symbol _inflateSetDictionary
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateSetDictionary
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
>> ld: warning multiple definitions of symbol _inflateInit2_
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateInit2_
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
>> ld: warning multiple definitions of symbol _inflateReset
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateReset
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
>> ld: warning multiple definitions of symbol _inflateInit_
>> /Library/Frameworks/R.framework/R(inflate.lo) definition of
>> _inflateInit_
>> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
>> ld: warning multiple definitions of symbol _adler32
>> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
>> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
>> ld: warning multiple definitions of symbol _BC
>> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
>> libreadline.4.3.dylib(terminal.so) definition of _BC
>> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
>> ld: warning multiple definitions of symbol _UP
>> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
>> libreadline.4.3.dylib(terminal.so) definition of _UP
>> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
>> ld: warning multiple definitions of symbol _PC
>> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
>> libreadline.4.3.dylib(terminal.so) definition of _PC
>> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
>> ld: warning multiple definitions of symbol _gzeof
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
>> ld: warning multiple definitions of symbol _gzclose
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
>> ld: warning multiple definitions of symbol _gzdopen
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
>> ld: warning multiple definitions of symbol _gzerror
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
>> ld: warning multiple definitions of symbol _gzflush
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
>> ld: warning multiple definitions of symbol _gzgetc
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
>> ld: warning multiple definitions of symbol _gzgets
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
>> ld: warning multiple definitions of symbol _gzopen
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
>> ld: warning multiple definitions of symbol _gzprintf
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
>> ld: warning multiple definitions of symbol _gzputc
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
>> ld: warning multiple definitions of symbol _gzputs
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
>> ld: warning multiple definitions of symbol _gzread
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
>> ld: warning multiple definitions of symbol _gzrewind
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
>> ld: warning multiple definitions of symbol _gzseek
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
>> ld: warning multiple definitions of symbol _gzsetparams
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
>> ld: warning multiple definitions of symbol _gztell
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
>> ld: warning multiple definitions of symbol _gzwrite
>> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
>> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
>> ** R
>> ** data
>> ** inst
>> ** save image
>> [1] TRUE
>> [1] TRUE
>> [1] TRUE
>> Loading required package: cluster
>> Loading required package: Biobase
>> Loading required package: tools
>> Welcome to Bioconductor
>> Vignettes contain introductory material. To view,
>> simply type: openVignette()
>> For details on reading vignettes, see
>> the openVignette help page.
>> [1] "propertyHolder"
>> [1] "property"
>> [1] "property"
>> [1] "property<-"
>> [1] "property<-"
>> [1] "asGraphProperty"
>> [1] "asGraphProperty"
>> [1] "asGraphProperty"
>> [1] "asGraphProperty"
>> [1] "asGraphProperty"
>> [1] "graph"
>> [1] "edgemode"
>> [1] "edgemode"
>> [1] "edgemode<-"
>> [1] "edgemode<-"
>> [1] "graphNEL"
>> [1] "initialize"
>> [1] "nodes"
>> [1] "nodes"
>> [1] "nodes<-"
>> [1] "nodes<-"
>> [1] "edges"
>> [1] "edges"
>> [1] "edges"
>> [1] "degree"
>> [1] "degree"
>> [1] "degree"
>> [1] "edgeWeights"
>> [1] "edgeWeights"
>> [1] "adj"
>> [1] "adj"
>> [1] "acc"
>> [1] "acc"
>> [1] "DFS"
>> [1] "DFS"
>> [1] "edgeL"
>> [1] "edgeL"
>> [1] "subGraph"
>> [1] "subGraph"
>> [1] "intersection2"
>> [1] "intersection2"
>> [1] "intersection"
>> [1] "intersection"
>> [1] "join"
>> [1] "join"
>> [1] "union"
>> [1] "union"
>> [1] "complement"
>> [1] "complement"
>> [1] "connComp"
>> [1] "connComp"
>> [1] "isConnected"
>> [1] "isConnected"
>> [1] "numNodes"
>> [1] "numNodes"
>> [1] "numNodes"
>> [1] "addNode"
>> [1] "addNode"
>> [1] "addNode"
>> [1] "removeNode"
>> [1] "removeNode"
>> [1] "clearNode"
>> [1] "clearNode"
>> [1] "removeEdge"
>> [1] "removeEdge"
>> [1] "addEdge"
>> [1] "addEdge"
>> [1] "combineNodes"
>> [1] "combineNodes"
>> [1] "inEdges"
>> [1] "inEdges"
>> [1] "inEdges"
>> [1] "inEdges"
>> [1] "show"
>> [1] "edgeNames"
>> [1] "edgeNames"
>> [1] "clusteringCoefficient"
>> [1] "clusteringCoefficient"
>> Error in assign("nullgraphID", getuuid()) :
>> couldn't find function "getuuid"
>> Execution halted
>> cat: ** Removing '/Users/mmccall/Library/R/library/graph'
>> ** Restoring previous '/Users/mmccall/Library/R/library/graph'
>> stdout: Broken pipe
>> ERROR: execution of package source for 'graph' failed
>> [1] "Attempting to download hexbin from
>> http://www.bioconductor.org/repository/devel/package/Source"
>> [1] "Download complete."
>> [1] "Installing hexbin"
>> * Installing *source* package 'hexbin' ...
>> ** libs
>> g77 -fno-common -g -O2 -c hbin.f -o hbin.o
>> ** Removing '/Users/mmccall/Library/R/library/hexbin'
>> make: g77: Command not found
>> make: *** [hbin.o] Error 127
>> ERROR: compilation failed for package 'hexbin'
>> ** Restoring previous '/Users/mmccall/Library/R/library/hexbin'
>> [1] "Attempting to download Ruuid from
>> http://www.bioconductor.org/repository/devel/package/Source"
>> [1] "Download complete."
>> [1] "Installing Ruuid"
>> * Installing *source* package 'Ruuid' ...
>> creating cache ./config.cache
>> checking for glib-config... no
>> checking how to run the C preprocessor... cc -E
>> checking for /usr/include/unistd.h... yes
>> updating cache ./config.cache
>> creating ./config.status
>> creating src/Makevars
>> ** libs
>> gcc -no-cpp-precomp
>> -I/Library/Frameworks/R.framework/Resources/include
>> -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include
>> -fno-common -g -O2 -c Rinit.c -o Rinit.o
>> In file included from Ruuid.h:5,
>> from Rinit.c:1:
>> uuidP.h:24:18: glib.h: No such file or directory
>> In file included from Ruuid.h:5,
>> from Rinit.c:1:
>> uuidP.h:36: error: parse error before "guint32"
>> uuidP.h:36: warning: no semicolon at end of struct or union
>> uuidP.h:37: warning: data definition has no type or storage class
>> uuidP.h:38: error: parse error before "time_hi_and_version"
>> uuidP.h:38: warning: data definition has no type or storage class
>> uuidP.h:39: error: parse error before "clock_seq"
>> uuidP.h:39: warning: data definition has no type or storage class
>> uuidP.h:40: error: parse error before "node"
>> uuidP.h:40: warning: data definition has no type or storage class
>> uuidP.h:41: error: parse error before '}' token
>> ** Removing '/Users/mmccall/Library/R/library/Ruuid'
>> ** Restoring previous '/Users/mmccall/Library/R/library/Ruuid'
>> make: *** [Rinit.o] Error 1
>> ERROR: compilation failed for package 'Ruuid'
>> From URL:
>> http://www.bioconductor.org/repository/devel/package/Source
>> graph version 1.4.22
>> hexbin version 1.1-2
>> Ruuid version 1.4.5
>>
>> Packages Rgraphviz and rhdf5 require special libraries to be
>> installed.
>> Please see the URL http://www.bioconductor.org/faq.html#Other Notes
>> for
>> more details on installing these packages if they fail
>> to install properly
>>
>> Warning messages:
>> 1: Installation of package graph had non-zero exit status in:
>> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
>> 2: Installation of package hexbin had non-zero exit status in:
>> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
>> 3: Installation of package Ruuid had non-zero exit status in:
>> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
>>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> --
> +----------------------------------------------------------------------
> -----+
> | Robert Gentleman phone : (617) 632-5250
> |
> | Associate Professor fax: (617) 632-2444
> |
> | Department of Biostatistics office: M1B20
> |
> | Harvard School of Public Health email: rgentlem at jimmy.harvard.edu
> |
> +----------------------------------------------------------------------
> -----+
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
---
Byron Ellis (ellis at stat.harvard.edu)
"Oook" -- The Librarian
------------------------------
Message: 16
Date: Thu, 28 Oct 2004 10:33:47 +0200
From: Martin Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [BioC] Color in the lefs of a dendrogram?
To: "Johan Lindberg" <johanl at biotech.kth.se>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <16768.44779.879793.334930 at gargle.gargle.HOWL>
Content-Type: text/plain; charset=us-ascii
Y
>>>>> "Johan" == Johan Lindberg <johanl at biotech.kth.se>
>>>>> on Wed, 27 Oct 2004 10:14:57 +0200 writes:
Johan> Hi all. I have a question of how to put color in a plot of a
Johan> hierarchical clustering that I have done with 24 microarrays in
an
Johan> experiment. The basic code that I use to plot:
Johan> sampdist <- dist(t(Mmatrix), method="euclidean")
Johan> sclus <- hclust(sampdist, method="average")
Johan> plot(sclus, cex=0.7)
Use dclus <- as.dendrogram(sclus)
and -- after reading help(dendrogram)
and maybe executing example(dendrogram)
use plot(dclus, ......................)
Martin Maechler, ETH Zurich
------------------------------
Message: 17
Date: Thu, 28 Oct 2004 10:42:52 +0200
From: Binita Dutta <binita.dutta at vib.be>
Subject: [BioC] Comparison of Affymetrix and CodeLink chip
To: bioconductor at stat.math.ethz.ch
Message-ID: <6.0.0.22.1.20041028104202.01ebd468 at 194.78.28.203>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Dear All,
I have been using limma for data analysis of affymetrix chips. We want to
compare result of affymetrix chip and Amersham Codelink. We have done
experiment with three knock out mice and compared with the wild type mice.
Can you suggest us the best bioconductor packages which can be used
to fish out differentially experessed genes with P. values on affymetrix
and codelink slides.
Help in this regard will be highly appreciated.
Binita
==============================
Binita Dutta, PhD
MicroArray Facility(MAF)
UZ Gasthuisberg
Onderwijs en Navorsing
Herestraat 49
3000 Leuven
Belgium
------------------------------
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