[BioC] Problem with limma2biomaRt and MBNI custom CDF

[James W. MacDonald]

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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