[BioC] AFFX probes as result of differential expression analysis

[Constanze Schmitt]

Hello,
I am doing a differential expression analysis on Affy HGU95A and
HGU95AV2 chips. After combining the data into one batch
(merge.AffyBatch)and jointly  normalising with rma (subsequent quality
check was ok), I used the "limma" package to fit a linear model (lmFit)
and then an empirical Bayes model(eBayes). Results are ranked with
topTable (fdr correction).
I get AFFX probes in my top 10 results; as far as I know these control
probes should not be differentially expressed. Does this hint at
possible batch-effects in my data even though there are no outlier chips
in the heatmap, intensity- and boxplots of the normalized chips?
I'd appreciate any help or ideas,
thanks,
Constanze





-- 
Dipl.-Bioinf. Constanze Schmitt

Technische Universität München
Institut für Informatik Lehrstuhl I12 - Bioinformatik
Boltzmannstr. 3
85748 Garching b. München, Germany

Room: MI 01.09.039 Phone: +49 (89) 289-19416 
Email: constanze.schmitt at in.tum.de
Web: http://wwwkramer.in.tum.de/people/schmittc