[BioC] RE: Bioconductor Digest, Vol 1, Issue 271
Huang, Cheng-Cheng (NIH/NCI)
huangc at mail.nih.gov
Fri Mar 21 06:20:03 MET 2003
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Subject: Bioconductor Digest, Vol 1, Issue 271
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Today's Topics:
1. Re: Bioconductor Digest, Vol 1, Issue 270 (Nicholas Lewin-Koh)
2. Affy package ?s (sorry for the repost) (Luckey, John)
3. Re: Affy package ?s (sorry for the repost) (Ben Bolstad)
4. mva functions (Jason Skelton)
5. Re: mva functions (Laurent Gautier)
----------------------------------------------------------------------
Message: 1
Date: Thu, 20 Mar 2003 05:04:06 -0800
From: "Nicholas Lewin-Koh" <nikko at hailmail.net>
Subject: [BioC] Re: Bioconductor Digest, Vol 1, Issue 270
To: bioconductor at stat.math.ethz.ch, bioconductor at stat.math.ethz.ch
Message-ID: <20030320130406.7C6822697B at www.fastmail.fm>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I don't think this is a g77 error, this is a linker error. I use redhat
linux myself so
I don't know much about the mandrake distribution. I would suggest first
following Laurent's advice and make sure that the readline libs are
installed on your system. As Laurent also comments nothing in
bioconductor is dependent on hexbin. But this will soon change and
hexagons will rule the world, na just kidding. If installing readline and
readline_devel doesn't help email again and i will see if we can't get
this debugged.
Nicholas
> Message: 1
> Date: Wed, 19 Mar 2003 17:10:23 +0100
> From: "buhard Ceph" <buhard at cephb.fr>
> Subject: [BioC] Install problem of some BioConductor packages
> under
> linux R session
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <001f01c2ee32$0d520610$4d05030a at cephb.fr>
> Content-Type: text/plain
>
> Hi all,
>
>
>
> I encounter some problems while trying to install BioConductor packages
> under R for Linux (perhaps as a new Bioconductor user, and not a linux
> expert !).
>
> I've downloaded the tar.gz file sources of Bioconductor and successfully
> installed a part of the bundle... but installation stops at 'hexbin',
> with an error indicating '-lreadline' is nof found, as reported here :
>
>
>
> After R CMD INSTALL treated 'graph' package, I get the following messages
> :
>
> * Installing *source* package 'hexbin' ...
> ** libs
> g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro
> -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame-pointer
> -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c
> hbin.f -o hbin.o
> g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro
> -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame-pointer
> -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c
> hcell.f -o hcell.o
> g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro
> -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame-pointer
> -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c
> herode.f -o herode.o
> g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro
> -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame-pointer
> -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c
> hsm.f -o hsm.o
> g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro
> -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame-pointer
> -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c
> htst.f -o htst.o
> gcc -shared -L/usr/local/lib -o hexbin.so hbin.o hcell.o herode.o hsm.o
> htst.o -L/usr/local/lib -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.2
> -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.2/../../.. -lreadline -ldl
> -lncurses -lfrtbegin -lg2c -lm -lgcc_s -L/usr/lib/R/bin -lR
> /usr/bin/ld: cannot find -lreadline
> collect2: ld returned 1 exit status
> make: *** [hexbin.so] Erreur 1
> ERROR: compilation failed for package 'hexbin'
> [root at localhost root]#
>
>
>
> None of all subsequent packages is installed then.
>
> Maybe there's something missing on my OS (mdk 9, kernel 2.4.19-24) ? Or a
> library with a bad (or missing) path declaration ? what else ?
>
> Any help greatly appreciated
>
> thanks in advance.
>
>
>
> BUHARD Olivier
> INSERM U434/CEPH
> 27 rue Juliette DODU
> 75010 PARIS
>
>
> [[alternate HTML version deleted]]
>
>
> ------------------------------
>
------------------------------
Message: 2
Date: Thu, 20 Mar 2003 11:42:05 -0500
From: "Luckey, John" <John.Luckey at joslin.harvard.edu>
Subject: [BioC] Affy package ?s (sorry for the repost)
To: <bioconductor at stat.math.ethz.ch>
Message-ID:
<AB77297D38B3B24C903DBFB2BBBBD7C8021338 at MAIL2.joslin.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hello Bioconductor Users,
Sorry to bother you, but I have a couple of quick questions on the affy
package that I have been unable to answer by reading through the textual
description of affy available on the bioconductor website and the recent
papers on the subject. Iin general, am very impressed with the noise
reduction using affy and truly appreciate the Bioconductor open source
concept and packages available. I am trying to compare directly our own
homebrewed data normalization within Splus (splining of affyIDs (post MAS
summing of probes)) with the rma output.
Question 1: Are the values output by rma to eset (and written to tab
delimited file with write.exprs) the logbase2 of the "actual" affyID values,
or are they the affyID values themselves. This is obviously important for
comparing rma to our old methods, and for estimates of "accurate" fold
change estimates- It seems to me that rma is much more precise in that much
of the noise between replicates, especially at the low end, seeems to have
been reduced in rma, but I am struggling with how to estimate back to
accurate fold change estimates.
Question 2: Is there an easy way to write out the PM values to tab delimited
file post background correction and normalization (to assess individual
probe sets prior to median polish). I am trying to work out reasons for
differences between our old method and rma for individual affy IDs.
Sincerely,
John Luckey
C John Luckey, MD PhD
Post Doctoral Fellow - Benoist-Mathis Lab
Joslin Diabetes Center
One Joslin Place, Rm. 474
Boston, MA 02215
phone: (617) 264-2783
fax: (617) 264-2744
e-mail: john.luckey at joslin.harvard.edu
------------------------------
Message: 3
Date: 20 Mar 2003 09:19:00 -0800
From: Ben Bolstad <bolstad at stat.berkeley.edu>
Subject: Re: [BioC] Affy package ?s (sorry for the repost)
To: "Luckey, John" <John.Luckey at joslin.harvard.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <1048180740.1645.120.camel at bmbbox.dyndns.org>
Content-Type: text/plain
>
> Question 1: Are the values output by rma to eset (and written to tab
delimited file with write.exprs) the logbase2 of the "actual" affyID
values, or are they the affyID values themselves. This is obviously
important for comparing rma to our old methods, and for estimates of
"accurate" fold change estimates- It seems to me that rma is much more
precise in that much of the noise between replicates, especially at the
low end, seeems to have been reduced in rma, but I am struggling with
how to estimate back to accurate fold change estimates.
>
The values given by the rma() function are log base 2. Working in log
base 2 you could take differences and then take 2^(difference) to get
fold changes. Or you could just take 2^(rma expression value) and take
ratios if you prefer.
You might find that RMA estimated fold changes are attenuated compared
to other methods. That is that the estimated fold change is smaller than
that computed using other methods. But the noise reduction at the low
end is pretty dramatic.
> Question 2: Is there an easy way to write out the PM values to tab
delimited file post background correction and normalization (to assess
individual probe sets prior to median polish). I am trying to work out
reasons for differences between our old method and rma for individual
affy IDs.
If you manually background correct and normalize (as individual steps),
doing something like
data <- ReadAffy()
data.bg <- bg.correct.rma(data)
data.norm.bg <- normalize(data,method="quantiles")
in each case pm(data.bg) and pm(data.norm.bg) will give pm matrices
after preprocessing. Investigate the function write.table() for
outputting the data to tab delimited files.
thanks,
Ben
------------------------------
Message: 4
Date: Thu, 20 Mar 2003 18:16:38 +0000 (GMT)
From: Jason Skelton <jps at sanger.ac.uk>
Subject: [BioC] mva functions
To: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.OSF.4.44.0303201809270.138580-100000 at pfes1.internal.sanger.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII
I'm trying to use the mva functions dist & hclust
however after a while I get the following message:
TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper =
FALSE)
Error: cannot allocate vector of size 589776 Kb
> typVSNcluster <- hclust(dist(typVSN at h))
Error: cannot allocate vector of size 589776 Kb
I'm running R in linux, any help much appreciated
regards
Jason
------------------------------
Message: 5
Date: Fri, 21 Mar 2003 03:29:33 +0100
From: Laurent Gautier <laurent at cbs.dtu.dk>
Subject: Re: [BioC] mva functions
To: Jason Skelton <jps at sanger.ac.uk>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <20030321022933.GB7797941 at genome.cbs.dtu.dk>
Content-Type: text/plain; charset=us-ascii
Dear Jason,
We would need to know a bit more about your settings,
like what one get by doing 'dim(typVSN)' or 'object.size(typVSN)',
and also the amount of RAM your machine has....
Hopin' it helps,
Laurent
On Thu, Mar 20, 2003 at 06:16:38PM +0000, Jason Skelton wrote:
>
>
> I'm trying to use the mva functions dist & hclust
> however after a while I get the following message:
>
> TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper =
> FALSE)
> Error: cannot allocate vector of size 589776 Kb
>
> > typVSNcluster <- hclust(dist(typVSN at h))
> Error: cannot allocate vector of size 589776 Kb
>
> I'm running R in linux, any help much appreciated
>
> regards
>
> Jason
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
--------------------------------------------------------------
currently at the National Yang-Ming University in Taipei, Taiwan
--------------------------------------------------------------
Laurent Gautier CBS, Building 208, DTU
PhD. Student DK-2800 Lyngby,Denmark
tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
------------------------------
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