[BioC] Problem with limma2biomaRt and MBNI custom CDF
James W. MacDonald
jmacdon at med.umich.edu
Tue Feb 6 18:32:23 CET 2007
Hi Scott,
This is a bug. The output from listAttributes() in biomaRt changed from
a vector to a matrix, and the code in limma2biomaRt() has to change to
accommodate that fact.
I will upload a bugfix to the release repository that will propagate in
time through the build process and be available via biocLite().
I will also send you a binary package (separately) that you can install
using the either the packages menu in RGui, or install.packages().
Best,
Jim
Ochsner, Scott A wrote:
> Hello,
>
> I get the following biomaRt error when trying to use the
> limma2biomaRt function in conjunction with a limma fit2 object
> created from a MBNI custom CDF. I thought I was faithfully following
> the "Annotating data with affycoretools and biomaRt" vignette.
>
> THE ERROR
>
>
>> limma2biomaRt(eset.mbni, fit2.mbni, design.mbni, cont.matrix.mbni,
>> species = "hsapiens",
>
> + pfilt = 0.05, interactive = FALSE) connected to: ensembl Reading
> database configuration of: hsapiens_gene_ensembl Checking main tables
> ... ok Checking attributes and filters ... ok Error: ' entrezgene 'is
> not an available annotation source for this biomaRt or this species.
> Available choices are listed below: name
> description 1 affy_hc_g110
> Affy hc g 110 ID(s) 2 affy_hg_focus
> Affy hg focus ID(s) 3 affy_hg_u133_plus_2
> Affy hg u133 plus 2 ID(s)
>
> ...cutoff for brevity.
>
> I'm fairly sure the gene IDs in fit2.mbni are indeed entrezgene IDs:
>
>
>
>> fit2.mbni$genes[1:5,]
>
> [1] "1_at" "10_at" "100_at" "1000_at" "10000_at"
>
> MY SESSION INFO AND ANALYSIS
>
>
>> sessionInfo()
>
> R version 2.4.0 (2006-10-03) 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] "tcltk" "splines" "tools"
> "methods" "stats" "graphics" "grDevices" "utils"
> "datasets" [10] "base"
>
> other attached packages: tkWidgets DynDoc
> widgetTools hgu133plus2cdf hs133phsentrezgcdf RMySQL
> "1.12.1" "1.12.0" "1.10.0" "1.14.0"
> "8.2.0" "0.5-11" DBI affycoretools biomaRt
> RCurl XML GOstats "0.1-12"
> "1.6.0" "1.8.0" "0.8-0" "1.2-0"
> "2.0.3" Category genefilter survival
> KEGG RBGL annotate "2.0.3" "1.12.0"
> "2.29" "1.14.0" "1.10.0" "1.12.0" GO
> graph limma affy affyio
> Biobase "1.14.0" "1.12.0" "2.9.1"
> "1.12.1" "1.2.0" "1.12.2"
>
>
>> library(affycoretools) eset.mbni <- justRMA(cdfname =
>> "hs133phsentrezgcdf",widget=T)
>
> Background correcting Normalizing Calculating Expression Warning
> message: Ambiguous method selection for "initialize", target
> "AffyBatch" (the first of the signatures shown will be used) exprSet
> VersionedBiobase Versioned in: .findInheritedMethods(classes, fdef,
> mtable)
>
>> dim(exprs(eset.mbni))
>
> [1] 17663 12
>
>> design.mbni<-model.matrix(~0+factor(rep(1:4, each=3)))
>> colnames(design.mbni)<-LETTERS[1:4]
>> cont.matrix.mbni<-makeContrasts(D-A, B-A,levels=design.mbni)
>> fit.mbni<-lmFit(eset.mbni,design)
>> fit2.mbni<-contrasts.fit(fit.mbni,cont.matrix)
>> fit2.mbni<-eBayes(fit2.mbni) limma2biomaRt(eset.mbni, fit2.mbni,
>> design.mbni, cont.matrix.mbni, species = "hsapiens",
>
> + pfilt = 0.05, interactive = FALSE) connected to: ensembl Reading
> database configuration of: hsapiens_gene_ensembl Checking main tables
> ... ok Checking attributes and filters ... ok Error: ' entrezgene 'is
> not an available annotation source for this biomaRt or this species.
> Available choices are listed below: name
> description 1 affy_hc_g110
> Affy hc g 110 ID(s) 2 affy_hg_focus
> Affy hg focus ID(s) 3 affy_hg_u133_plus_2
> Affy hg u133 plus 2 ID(s)
>
>
>
> Scott A. Ochsner, Ph.D. NURSA Bioinformatics Molecular and Cellular
> Biology Baylor College of Medicine Houston, TX. 77030 phone:
> 713-798-6227
>
> _______________________________________________ Bioconductor mailing
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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