[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
## 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():
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 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
 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):
 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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