which expression levels should I choose in microarray?

Question

[cagdas]

Hi, I am looking for genes that have altered expression levels. When I use GEO database, I find multiple results for same gene within one dataset. Which of them should I use?

If I choose their average or highest value, how can I filter them?

Thanks for your help

Answer 1

[h.mon]

The R/BioConductor package limma has the avereps(). See a good answer at How to combine expression values of multiple probes for one gene? .