differential expression analysis with z score normalized microarray data
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
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