[BioC] Automation Server for R?
MOConnell at insightful.com
moconnell at insightful.com
Tue Mar 25 08:55:03 MET 2003
Hi Richard
I can discuss BioConductor/ArrayAnalyzer and porting of R scripts to S-PLUS
and vice-versa with you off-line if you like. Im also giving a half-day
seminar in Boston this Friday on: "Analysis of Microarray Data Using S-PLUS,
R and S+ArrayAnalyzer", where I'll be discussing ArrayAnalyzer and
BioConductor. Let me know if you'd like to attend.
http://www.insightful.com/company/eventdescription.asp?EID=57
Michael
Michael O'Connell, Ph.D. moconnell at insightful.com
Director, BioPharm Solutions www.insightful.com
Insightful Corporation
2505 Meridian Parkway Suite 175
Durham NC 27713
ph. 919-5725545
Message: 1
Date: Mon, 24 Mar 2003 11:56:10 -0500 (EST)
From: Vincent Carey 525-2265 <stvjc at channing.harvard.edu>
Subject: Re: [BioC] Automation Server for R?
To: "Park, Richard" <Richard.Park at joslin.harvard.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.GSO.4.40.0303241152250.28136-100000 at capecod.bwh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
For R-S interfaces, see www.omegahat.org/RinS
As for comprehensive porting to S-plus, probably
best to contact Insightful directly
What is an "Automation server"?
---
Vince Carey, PhD
Ass't Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu
On Fri, 21 Mar 2003, Park, Richard wrote:
> Does anyone know of a package for R that allows for it to run as an
> Automation Server? Or of any wrapper/interface that would allow
> S-plus to interact with R? I am trying to compare methods of using
> the scripts that are part of the bioconductor package (i.e.
> ArrayAnalyzer, and this interface). Or does anyone know of
> anyone porting all the R scripts into S-plus.
>
> Thanks,
> Richard Park
> Computational Data Analyzer
> Joslin Diabetes Center
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
------------------------------
Message: 2
Date: 24 Mar 2003 09:08:52 -0800
From: Ben Bolstad <bolstad at stat.berkeley.edu>
Subject: Re: FW: [BioC] get all NaN values
To: Sue Kong <Sue.Kong at cchmc.org>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <1048525732.1219.51.camel at bmbbox.dyndns.org>
Content-Type: text/plain
On Mon, 2003-03-17 at 12:11, Sue Kong wrote:
> I reinstalled Bioconductor and loaded Affy package 1.2.2 this afternoon
> but still get this NaN value problem. When will be the fixed affy
> version available?
> Thanks
> Sue
Please revert to using the Release version of the affy package for now.
When the automated build process picks up a new version, you can go back
to the development version
Thanks,
Ben
------------------------------
Message: 3
Date: Mon, 24 Mar 2003 12:13:31 -0500 (EST)
From: Jeff Gentry <jgentry at jimmy.harvard.edu>
Subject: Re: [BioC] Install problem of some BioConductor packages
under linux R session
To: buhard Ceph <buhard at cephb.fr>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.SOL.4.20.0303241213000.19501-100000 at santiam.dfci.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> 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 ?
You need the readline library. This is discussed in the R-FAQ, question
7.22 ...
http://cran.r-project.org/doc/FAQ/R-FAQ.html
------------------------------
Message: 4
Date: Mon, 24 Mar 2003 12:31:47 -0500 (EST)
From: Jeff Gentry <jgentry at jimmy.harvard.edu>
Subject: Re: [BioC] PRgSQL
To: Qi Sun <qisun at tc.cornell.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.SOL.4.20.0303241226310.19501-100000 at santiam.dfci.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> I got this error message:
> Package AnnBuilder version 1.0.2 requires package RPgSQL
> in: resolve.depends(pkgInfo, repEntry, force, searchOptions =
searchOptions,
>
> I was not able to download the RPgSQL package for windows
> anywhere. the CRAN page said the RPgSQL is not supported, and the
RPgSQL does not exist for Windows, as far as I know.
I believe (although Jianhua Zhang will know far better then I) that it is
not required for Annbuilder under Windows.
For now, it is probably easiest to manually download the Annbuilder
package
at:
http://www.bioconductor.org/repository/release1.1/package/html/AnnBuilder.ht
ml
-Jeff
------------------------------
Message: 5
Date: Mon, 24 Mar 2003 12:32:33 -0500
From: Kelvin Yen <kelvin.yen at mssm.edu>
Subject: [BioC] MAS on Bioconductor
To: bioconductor at stat.math.ethz.ch
Message-ID: <98B236D8-5E1E-11D7-9AA6-003065F47230 at mssm.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi,
I'm a new user to Bioconductor and I've been using the Affy package to
analyze the .Cel files I have. I tried replicating the analysis I did
using Affy's MAS program with bioconductor's MAS algorithm but the
results I get are completely different than the ones I get using the
original MAS software. I'm analyzing six .Cel files and using MAS and
a subsequent t-test on the values, I get many(~30) values that are
e-05. But using Bioconductor's MAS algorithm, I only get one. Here
are the commands that I'm using to generate the data.
Data <- ReadAffy()
eset <- expresso(Data, normalize=FALSE, bgcorrect.method="mas",
pmcorrect.method="mas, summary.method="mas")
eset <- affy.scalevalue.exprSet(eset)
write.exprs(eset, file="mas.xls")
I'm using the MGU74aV2 chip. Any help would be greatly appreciated.
Kelvin Yen
PS I eventually wanted to run the RMA algorithm on my data but first
wanted to make sure I could replicate data that I already knew the
value to.
------------------------------
Message: 6
Date: Mon, 24 Mar 2003 13:14:28 -0500 (EST)
From: Vincent Carey 525-2265 <stvjc at channing.harvard.edu>
Subject: Re: [BioC] Cannot load widgetTools package
To: "Gunter, Bert" <bert_gunter at merck.com>
Cc: "'bioconductor at stat.math.ethz.ch'"
<bioconductor at stat.math.ethz.ch>
Message-ID:
<Pine.GSO.4.40.0303241311090.21030-100000 at capecod.bwh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
i see that addVig2Menu is a function in Biobase 1.3.10 --
it may be present in earlier versions, but it seems not to
be present in 1.1.2.
the interdependency control for installations and attachments
is an infrastructure project under way at Bioconductor in
conjunction with R core. You may be able to get away
with
getBioC("prog", isDevel=TRUE, force=TRUE)
which I believe will get you a new Biobase and should
leave the other packages alone ... or you could manually
bring in the newer Biobase zip archive
keep us posted.
---
Vince Carey, PhD
Ass't Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu
On Fri, 21 Mar 2003, Gunter, Bert wrote:
> Platform: Winnt , R1.6.2, BioBase 1.1.2, ReposTools 1.1.15, tkWidgets
1.0.2,
> tcktk 8.3.4
>
> Note: Please reply directly, as I was unable to subscribe to the newslist.
> This was because the BioConductor email web page interface did not accept
my
> email address as valid for some unknown reason when I tried to subscribe.
> (presumably a bug there). No matter -- I only wanted to post this message,
> anyway.
>
> My problem: I downloaded and installed the the tkWidgets package both via
> the getBioC and downloaded zip file processes, but ran into the same
problem
> both ways, to whit:
>
> library(widgetTools)
>
> Error in firstlib(which.lib.loc, package) :
> couldn't find function "addVig2Menu"
> Error in library(widgetTools) : .First.lib failed
>
> Et tu, Brute ?
>
> Cheers,
> Bert Gunter
> Biometrics Research RY 84-16
> Merck & Company
> P.O. Box 2000
> Rahway, NJ 07065-0900
> Phone: (732) 594-7765
> mailto: bert_gunter at merck.com
>
> "The business of the statistician is to catalyze the scientific learning
> process." -- George E.P. Box
>
>
>
>
----------------------------------------------------------------------------
--
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
------------------------------
Message: 7
Date: Mon, 24 Mar 2003 14:53:29 -0500 (EST)
From: "Rafael A. Irizarry" <ririzarr at jhsph.edu>
Subject: Re: [BioC] MAS on Bioconductor
To: Kelvin Yen <kelvin.yen at mssm.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.LNX.4.33.0303241452500.31050-100000 at localhost.localdomain>
Content-Type: TEXT/PLAIN; charset=US-ASCII
for the answer to your mas 5 question read this:
http://stat-www.berkeley.edu/users/bolstad/MAS5diff/Mas5difference.html
for writing pms to delimeted use the "pm" function to extract the pms
out of your affybatch, for example:
Data <- ReadAffy()
pms <- pm(Data)
and read the help file on write.table.
On
Mon, 24 Mar 2003, Kelvin
Yen wrote:
> Hi,
>
> I'm a new user to Bioconductor and I've been using the Affy package to
> analyze the .Cel files I have. I tried replicating the analysis I did
> using Affy's MAS program with bioconductor's MAS algorithm but the
> results I get are completely different than the ones I get using the
> original MAS software. I'm analyzing six .Cel files and using MAS and
> a subsequent t-test on the values, I get many(~30) values that are
> e-05. But using Bioconductor's MAS algorithm, I only get one. Here
> are the commands that I'm using to generate the data.
>
> Data <- ReadAffy()
> eset <- expresso(Data, normalize=FALSE, bgcorrect.method="mas",
> pmcorrect.method="mas, summary.method="mas")
> eset <- affy.scalevalue.exprSet(eset)
> write.exprs(eset, file="mas.xls")
>
> I'm using the MGU74aV2 chip. Any help would be greatly appreciated.
>
> Kelvin Yen
> PS I eventually wanted to run the RMA algorithm on my data but first
> wanted to make sure I could replicate data that I already knew the
> value to.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
------------------------------
Message: 8
Date: Mon, 24 Mar 2003 15:49:05 -0500
From: "Luckey, John" <John.Luckey at joslin.harvard.edu>
Subject: [BioC] Replicate quality assessment?
To: <bioconductor at stat.math.ethz.ch>
Message-ID:
<AB77297D38B3B24C903DBFB2BBBBD7C802133D at MAIL2.joslin.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hello all,
I am looking for a quantitative measure of replicate quality to know if one
should be tossed or not. Right now, its a gestalt from pairs and mva plots
after running rma on datasets across all replicates and covariates. Would
like your experience on reasonable method for quantifying "goodness of
replication".
Idea one: simply to use variance measure displayed in mva.pairs plots (This
is function of my statistically ignorant empirical assessment- most
replicates seem to fall <0.4 while between covariates is usually >.45).
Alternate method might be use the slope of the fitted line on qq plots (or y
intercept) of the M values? Does that measure sound at all reasonable? Is
there any real difference between this and variance measurement above?
Towards that end, I have been working with data in S-plus and making qq
plots there on M values, is there easy way (ie function) within R to go from
exprs values to qq plots of M values (or for that matter- to easily go from
exprset object to MVA and QQ plots between covariates?)
Tnaks in advance for your advice,
John
------------------------------
Message: 9
Date: Mon, 24 Mar 2003 16:42:59 -0500
From: DMITRY GRIGORYEV <dgrigor1 at jhmi.edu>
Subject: [BioC] One run and dead
To: bioconductor at stat.math.ethz.ch
Message-ID: <271f49274c7d.274c7d271f49 at jhmimail.jhmi.edu>
Content-Type: text/plain; charset=us-ascii
Hi!
I am running Bioconductor on WindowsXP and can do just one job at a time.
When I've submitted another job my machine got memory problem (I have 1G of
RAM though). I am exiting Bioconductor and open it again. Memory problem
is fixed by this (is there hanging pointers somewhere?) but affy library is
screwed.
This what I have:
Error in mlistMetaName(f) : No way to associate a generic function with an
object of class "NULL"
Error in library(affy) : .First.lib failed
The only way I can fix it is to reinstall whole package again.
Is there Uninstall function for Bioconductor, which will not uninstall R?
How to fix described problem?
How much memory should I have to run 33 U133 chips at once?
Thank you
Dmitry N. Grigoryev, M.D., Ph.D.
Data Analyst
Gene Expression Profiling Core
Division of Pulmonary and Critical Care Medicine
Johns Hopkins University School of Medicine
------------------------------
Message: 10
Date: Mon, 24 Mar 2003 17:09:32 -0500 (EST)
From: Vincent Carey 525-2265 <stvjc at channing.harvard.edu>
Subject: Re: [BioC] One run and dead
To: DMITRY GRIGORYEV <dgrigor1 at jhmi.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.GSO.4.40.0303241705001.235-100000 at capecod.bwh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> Hi!
> I am running Bioconductor on WindowsXP and can do just one job at a time.
When I've submitted another job my machine got memory problem (I have 1G of
RAM though). I am exiting Bioconductor and open it again. Memory problem
is fixed by this (is there hanging pointers somewhere?) but affy library is
screwed.
> This what I have:
>
> Error in mlistMetaName(f) : No way to associate a generic function with an
object of class "NULL"
> Error in library(affy) : .First.lib failed
For this sort of thing you have to tell us the versions of the various
tools you are working with: What version of R, which version of affy,
etc. The errors above have to do with the methods package of R
which is evolving independently of affy.
>
> The only way I can fix it is to reinstall whole package again.
this is overkill. you have to provide more precise diagnostic
information to solve the problem rationally.
>
> Is there Uninstall function for Bioconductor, which will not uninstall R?
> How to fix described problem?
no. but you could use Rcmd REMOVE [pkgname] from a windows
DOS prompt if you had Rcmd.exe in your path.
------------------------------
Message: 11
Date: Mon, 24 Mar 2003 20:10:50 -0700 (MST)
From: Karen.Chancellor at asu.edu
Subject: [BioC] feature selection
To: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.GSO.4.21.0303242008050.16516-100000 at general2.asu.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Hello Bioconductor folk,
Can any of the bioconductor packages be used on a .pcl file, rather than
starting with the raw data?
I am starting with a .pcl file containing approximately 900 genes and 50
samples, which I have read using read.table. The classification is known,
and
there are 3 classes of samples. I am interested in reducing the number of
genes. I would like to use the R RandomForest package for this task.
Is this appropriate? I'm new to this so will appreciate any help.
Thanks
Karen
.- --. ....- -.-. -.-.
------------------------------
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