[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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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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