[BioC] Problem with limma2biomaRt and MBNI custom CDF

[Ochsner, Scott A]

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