Dear all,

Following the RMA normalization of data from Affy Human Exon ST1.0 array
using the package Oligo (at the transcript level using target="core"), I
then conducted a limma analysis.

The topTable argument in limma would then retrieve the top genes (in my
case, cause I am interested in subsequently doing GSEA analysis, I set
number=100) which are differentially addressed.

The question I have is how can I map the Affy ID which is found in the
results from topTable to an ENSEMBL and an ENTREZ gene ID. Intuitively,
biomaRt comes to mind, and I did a biomaRt query for the list of top 100
genes which I had gotten, but I get only 14 hgnc symbols. I'd like to think
that it's due to a lack of annotations, but I highly doubt so (14 in a list
of 100 seems too little to me).

My code for biomaRt is as follows:
mart <- useMart("ensembl", "hsapiens_gene_ensembl")

hgnc <- getBM(attributes=c("hgnc_symbol",
"ensembl_gene_id"),values=top100$ID, filters="affy_huex_1_0_st_v2",
mart=mart)

I was wondering 2 things:
1. Is there any plausible explanation to why the query only returns 14 IDs;
and
2. Are there other ways that I can use to fetch annotations from a
post-Limma analysis?

My session info is as follows:
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

Thanks for any advice!

Jeremy

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