[BioC] avereps function

[Erika Melissari]

 Dear list,

does anyone use avereps function by limma package to average probe copies on 
microarray?
I used this function and obtained a strange result: my differentially 
expressed gene list sensibly change if I use or not this function (I perform 
the average before lmFit and after normalization).
I know this function only averages probe copies that are on a microarray, 
also if they are in multiple not fixed number.
What is the problem?
Thank you very much

Erika