What open software have you used for microarray analysis?
I am using custom made arrays and can easily extract matrices of gene expression levels for each individual and each gene.
I am looking for a replacement for the R-maanova package that we have been using for years now in the lab, but given our good experience with this one, I don't want to waste time trying to learn an only half-assed solution. :)
So, what have you used that you would unconditionally recommend?