[BioC] mouse4302,db_2.0.2 in AffylmGUI #2
Keith Satterley
keith at wehi.EDU.AU
Thu Apr 10 02:38:36 CEST 2008
Hi Richard,
On reflection, the problem is that affylmGUI is reading the chip name etc. from
your data. As you have found, if affylmGUI can't find a package it wants, it
goes and gets it and installs it.
I've included a little script I have used to check data that I am testing.
I don't have any mouse4302 data available to test exactly what it would return.
Create a targets.txt file for your data files, like the one described below.
Modify Section 1 suit your situation.
Run R and paste Section 1 into your R session.
#Section 1.
###########
#Test script for reading data into affylmGUI
#No need to run affylmGUI, just load it and its dependencies.
library(affylmGUI)
#
setwd("W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files")
TargetsFile <- "targets.txt"
Targets <- read.table(TargetsFile,header=TRUE,sep="\t",quote="\"",as.is=TRUE)
Targets$FileName
#
#RAD is the name for the RawAffyData
RAD <- ReadAffy(filenames=Targets$FileName)
#
SlideNamesVec <- colnames(exprs(RAD))
SlideNamesVec
#
Targets$Name
if("Name" %in% colnames(Targets))SlideNamesVec <- Targets$Name
#Show SlideNamesVec
SlideNamesVec
#
#Show the RAD object
RAD
#Try some methods on the AffyBatch
cdfName(RAD)
#
#Section 2.
###########
boxplot(RAD)
#
NormalizationMethod <- "RMA"
rmaRAD <- rma(RAD)
NormrmaRAD.exprs <- exprs(rmaRAD)
NormrmaRAD.se.exprs <- NULL
summary(NormrmaRAD.exprs)
summary(NormrmaRAD.se.exprs)
#
NormalizationMethod <- "GCRMA"
Require("gcrma")
gcrmaRAD <- gcrma(RAD)
NormgcrmaRAD.exprs <- exprs(gcrmaRAD)
NormgcrmaRAD.se.exprs <- NULL
summary(NormgcrmaRAD.exprs)
summary(NormgcrmaRAD.se.exprs)
#
NormalizationMethod <- "affyPLM"
Require("affyPLM")
Pset <- fitPLM(RAD)
NormPset.exprs <- coefs(Pset)
NormPset.se.exprs <- se(Pset)
summary(NormPset.exprs)
summary(NormPset.se.exprs)
#
############
My targets.txt contents was:
Name FileName Target
Abs10.1 low10-1.cel EstAbsent10
Abs10.2 low10-2.cel EstAbsent10
Pres10.1 high10-1.cel EstPresent10
Pres10.2 high10-2.cel EstPresent10
Abs48.1 low48-1.cel EstAbsent48
Abs48.2 low48-2.cel EstAbsent48
Pres48.1 high48-1.cel EstPresent48
Pres48.2 high48-2.cel EstPresent48
Modify the script to suit your situation and run Section 1.
This may explain which version of mouse4302 is needed with your data.
Section 2. is for further investigation if you wish.
cheers,
Keith
Richard Friedman wrote:
> On Apr 8, 2008, at 8:19 PM, Keith Satterley wrote:
>> Richard,
>>
>> You don't supply output from sessionInfo() so I can't tell what
>> versions you have.
>>
>> packageDescription("mouse4302.db")
>>
>> will give you information about your currently installed
>> mouse4302.db package.
>>
>> To install mouse4302.db, use:
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("mouse4302.db")
>>
>> I'm using R-2.6.2 on Windows and it installed:
>> http://bioconductor.org/packages/2.1/data/annotation/bin/windows/
>> contrib/2.6/mouse4302.db_2.0.2.zip
>>
>>
>> hope that helps
>>
>> cheers,
>
> Keith,
>
> I had installed mouse4302.db_2.0.2.. My problem is that AffylmGUI keeps
> reading mouse4302_2.0.1 instead.
>
>
> I tried to read mouse4302.db_2.0.2 twice. The first time I loaded it,
> prior to running toptable in afflymGUI. Here is a partial record of
> that session.
>
> Loading required package: mouse4302
>
>
>
> Attaching package: 'mouse4302'
>
>
>
>
>
> The following object(s) are masked from package:mouse4302.db :
>
>
>
> mouse4302ACCNUM,
>
> mouse4302CHR,
>
> mouse4302CHRLENGTHS,
>
> mouse4302CHRLOC,
>
> mouse4302ENTREZID,
>
> mouse4302ENZYME,
>
> mouse4302ENZYME2PROBE,
>
> mouse4302GENENAME,
>
> mouse4302GO,
>
> mouse4302GO2ALLPROBES,
>
> mouse4302GO2PROBE,
>
> mouse4302MAP,
>
> mouse4302MAPCOUNTS,
>
> mouse4302ORGANISM,
>
> mouse4302PATH,
>
> mouse4302PATH2PROBE,
>
> mouse4302PFAM,
>
> mouse4302PMID,
>
> mouse4302PMID2PROBE,
>
> mouse4302PROSITE,
>
> mouse4302REFSEQ,
>
> mouse4302SYMBOL,
>
> mouse4302UNIGENE
>
>
>
>
>
>
>
> > sessionInfo()
>
> R version 2.6.1 (2007-11-26)
>
> i386-pc-mingw32
>
>
>
> locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
> 1252;LC_MONETARY=English_United States.
> 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>
>
> attached base packages:
>
> [1] splines tcltk tools stats graphics grDevices utils
>
> [8] datasets methods base
>
>
>
> other attached packages:
>
> [1] mouse4302_2.0.1 mouse4302probe_2.0.0 mouse4302cdf_2.0.0
>
> [4] gcrma_2.10.0 matchprobes_1.10.0 affylmGUI_1.12.0
>
> [7] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1
>
> [10] limma_2.12.0 mouse4302.db_2.0.2 AnnotationDbi_1.0.6
>
> [13] RSQLite_0.6-8 DBI_0.2-4 Biobase_1.16.3
>
>
>
> loaded via a namespace (and not attached):
>
> [1] rcompgen_0.1-17
>
> Warning messages:
>
> 1: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
>
> Estimation of var.prior failed - set to default value
>
> 2: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
>
> Estimation of var.prior failed - set to default value
>
> >
>
> As far as I can when I ran toptable in AffylmGUI the program
> automatically loaded
>
>
> mouse4302_2.0.1 and ignored mouse mouse4302.db_2.0.2.
>
> The second time I ran it, I removed mouse4302_2.0.1 from the library,
> leaving only mouse4302.db_2.0.2. .Again, when I ran toptable the program
> automatically installed mouse4302_2.0.1.
>
>
> attached base packages:
>
> [1] splines tools tcltk stats graphics grDevices utils
>
> [8] datasets methods base
>
>
>
> other attached packages:
>
> [1] mouse4302_2.0.1 mouse4302probe_2.0.0 mouse4302cdf_2.0.0
>
> [4] gcrma_2.10.0 matchprobes_1.10.0 affylmGUI_1.12.0
>
> [7] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1
>
> [10] Biobase_1.16.3 limma_2.12.0
>
> Warning messages:
>
> 1: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
>
> Estimation of var.prior failed - set to default value
>
> 2: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
>
> Estimation of var.prior failed - set to default value
>
>
>
> My question: Is there any way that I can get AffylmGUI to use
>
> mouse4302.db_2.0.2. as annotation?
>
> Thanks and best wishes,
> Rich
>
>> Keith
>>
>> ========================
>> Keith Satterley
>> Bioinformatics Division
>> The Walter and Eliza Hall Institute of Medical Research
>> Parkville, Melbourne,
>> Victoria, Australia
>> =======================
>>
>> Richard Friedman wrote:
>>> Dear Bioconductor users,
>>> I want the most uptodate annotation for the mouse 4302 chip.
>>> As far as know that is mouse4302,db_2.0.2. However when I use
>>> AffylmGUI it automatically loads mouse4302_2.0.1.
>>> My questions:
>>> 1. Is there any way to get afflmGUI to load mouse4302,db_2.0.2
>>> instead.
>>> OR
>>> 2. Failing, that I have not been able to combine the limma output
>>> with
>>> selected columns of the annotation in the R command line.
>>> Pragmatically
>>> I have been using afflmGUI to get the annotation file or
>>> downloading it from
>>> thee affy web site and merging it in excel. any quick code to do this
>>> entirely in the command line would be appreciated. I have not been
>>> successful in applying the code in "Bioinformatics and Computational
>>> Biology Solutions..." to this purpose.
>>> Any suggestions would be appreciated.
>>> Thanks and best wishes,
>>> Rich
>>> ------------------------------------------------------------
>>> Richard A. Friedman, PhD
>>> Associate Research Scientist,
>>> Biomedical Informatics Shared Resource
>>> Herbert Irving Comprehensive Cancer Center (HICCC)
>>> Lecturer,
>>> Department of Biomedical Informatics (DBMI)
>>> Educational Coordinator,
>>> Center for Computational Biology and Bioinformatics (C2B2)/
>>> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
>>> Box 95, Room 130BB or P&S 1-420C
>>> Columbia University Medical Center
>>> 630 W. 168th St.
>>> New York, NY 10032
>>> (212)305-6901 (5-6901) (voice)
>>> friedman at cancercenter.columbia.edu
>>> http://cancercenter.columbia.edu/~friedman/
>>> In Memoriam,
>>> Arthur C. Clarke
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>> gmane.science.biology.informatics.conductor
>
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