Hello,

I'm analyzing human exon arrays normalized using Affymetrix Power tools 
for normalization (using 'core' probes) and limma for significantly 
modulated genes (all at the gene level, of course).

The limma2annaffy function produce tables, but with all annotation table 
cells empty. I'm doing:

limma2annaffy(eSet.gene, fit2, design,cont.matrix, lib = 
"huex10stv2hsentrezg.db", interactive=F, pfilt=0.05, fldfilt=0.8)

where huex10stv2entrezg.db is from : 
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/entrezg.asp

Is it the right file to use?

Using onechannelGUI produce the same tables but with annotations, so I 
know there's a way to do it.

To complicate things further, limma2biomaRt, which is another option, 
fails with:

    "Request to BioMart web service failed. Verify if you are still
    connected to the internet.  Alternatively the BioMart web service is
    temporarily down."

which from the mailing list seem to be an RCurl problem. I tried 
updating it to the latest and older (0.92) versions, using --internet2 
doesn't solve this and as far as I know i'm not using a proxy to connect 
to the net. I'm under Windows 7.

Any help would be appreciated,
Michael

	[[alternative HTML version deleted]]

