[BioC] Exon array annotation with limma?
James W. MacDonald
jmacdon at med.umich.edu
Mon Dec 21 19:01:14 CET 2009
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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>
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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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