[BioC] Exon array annotation with limma?

[Michael Imbeault]

Thanks for the help James,

I did:

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

(note the  sep="", without it the probes were like "1000 _at"). Sadly, 
the end result is the same, except that as a side effect, the first 
column probe links don't work anymore (because of the added _at, they 
don't link to the right probe on the Affy site).

I verified that the probes in eSet.gene contain _at after the operation. 
I build my eset with:

eSet.gene <- new("ExpressionSet", exprs = rma.gene, phenoData = phenoData)

Should I add annotation="huex10stv2" or "huex10stv2hsentrezg" or 
something similar? Do i need the cdf file in addition to the .db one?

Thanks,
Michael

On 21/12/2009 1:01 PM, James W. MacDonald wrote:
> 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
>>
>>     [[alternative HTML version deleted]]
>>
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>