[BioC] mouse4302,db_2.0.2 in AffylmGUI #2
Richard Friedman
friedman at cancercenter.columbia.edu
Wed Apr 9 17:54:57 CEST 2008
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
>> _______________________________________________
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