Entering edit mode
Scott Ochsner
▴
300
@scott-ochsner-599
Last seen 10.3 years ago
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
