differential expression analysis with z score normalized microarray data

Question

[gracie]

Hi all,

I am dealing with a Z normalized expression dataset and I want to perform differential expression analysis with two factor . I tried limma with two factor design (and also single) but couldnt find any gene altered significantly.

I am not sure is it because I am violating any assumptions of limma. Is there any other way for such analysis or any suggestions for the normalization of custom made microarray?

Thanks in advance

[ATpoint]

Why not simply feeding the raw data into the common microarray workflows?