[BioC] limma: topTable

[Gordon Smyth]

At 02:32 AM 19/03/2004, Julia Engelmann wrote:
>Hi Bioconductor folks,
>
>I have really been enjoying using the limma package, but I have just come
>across a problem.
>When I use the topTable-command, the slot "result$Probe.Set.ID" does not seem
>to match the other entries I am interested in, namely M, P, t.
>I am using R 1.8.0, limma 1.5.5 on Affymetrix ATH1-121501 chips.
>
>An example would be:
>Output of the topTable-result:
>
>                 Probe.Set.ID            M               t 
> P.Value         B
>5598    259302_at       4.593339 38.9793 1.126260e-05 11.88238
>
>If I check on gene number 5598 it says
>geneNames(myExprSet)[5598]
>[1] "250498_at"
>
>Am I misinterpreting 5598 as the index of my ExpressionSet?

I think you've done something non-standard, anyway you can't have simply 
used lmFit() and eBayes() and topTable() on our exprSet object. Please show 
us enough of your code so that we can see how topTable is getting the probe 
set ID's.

Gordon

>Thanks a lot for any suggestions!
>Julia