[BioC] Exon array annotation with limma?

[James W. MacDonald]

Hi Michael,

Michael Imbeault wrote:
> 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?

Most likely. However, the MBNI folks have an unfortunate habit of adding 
_at to the end of all their probesets, regardless the source. So for 
instance, if I look at the probesets in this package, I get something 
like this:

 > head(Lkeys(huex10stv2hsentrezgGENENAME))
[1] "10000_at"     "10001_at"     "10002_at"
[4] "100033423_at" "100033424_at" "100033425_at"

And I am betting if you do something like head(featureNames(eSet.gene)), 
you won't have any of those nasty _at extensions.

A simple albeit kludgy fix would be for you to first do

featureNames(eSet.gene) <- paste(featureNames(eSet.gene), "_at")

and then run limma2annaffy().
> 
> Using onechannelGUI produce the same tables but with annotations, so I 
> know there's a way to do it.

I am betting that the onechannelGUI folks know about the extra _at 
extensions and are silently stripping them. I could hypothetically do 
the same, but I rebel against the idea that I should have to put code in 
my package to protect people from infelicities in other people's packages.


Best,

Jim


> 
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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