[BioC] Annotation databases--unable to get annotations

Manjula Kasoji [guest] guest at bioconductor.org
Wed Oct 10 20:31:25 CEST 2012

Has anyone used the mogene10stprobeset.db annotation package?

I have a list of significant probeset ids that I obtained from running an analysis in the limma package. When I try to use mget() to retrieve the corresponding gene names only a couple of probesets get annotated. I've tried with several different gene lists. In a gene list of about 300 genes, only 2 get annotated at the most. The rest of the probesets get a "NA" for the annotation.

Here is my R code:

## load library
> library("mogene10stprobeset.db")

## map probe ids to gene names...

#extract ids from signifcant gene list

#if not in character form, change to character
ids = as.character(ids)

#retrieve gene names from annotation package for ids in signficant gene list
mget(ids, mogene10stprobesetGENENAME, ifnotfound=NA)

I've tried ENTREZID, SYMBOL, and GO, all of them return annotations just for a few probesets.

I'm using R version R 2.15.1 for Macs.

Any help would be appreciated!!


 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu95av2.db_2.7.1           org.Hs.eg.db_2.8.0          limma_3.14.0                mogene10stv1cdf_2.11.0      affy_1.36.0                 mogene10stprobeset.db_8.0.1 org.Mm.eg.db_2.8.0         
 [8] RSQLite_0.11.2              DBI_0.2-5                   AnnotationDbi_1.20.0        Biobase_2.18.0              BiocGenerics_0.4.0          BiocInstaller_1.8.2        

loaded via a namespace (and not attached):
[1] affyio_1.26.0         IRanges_1.16.2        parallel_2.15.1       preprocessCore_1.20.0 stats4_2.15.1         tools_2.15.1          zlibbioc_1.4.0       

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