[BioC] limma: topTable

[Julia Engelmann]

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?

Thanks a lot for any suggestions!
Julia