Hello everyone,

I want to do a differential coexpression analysis to a microarray data. My data have rows for genes and columns for conditions. 30 control and 28 disease columns. 

I checked some packages such as WGCNA but I think they don't take expression data as input.

Anyone has any advice, tutorial or another package to do it?

Thanks.

Searching for "differential coexpression" brings out several articles describing different ways of doing a differential co-expression analysis.

WGCNA is not designed for gene-level differential co-expression analysis, but you can certainly study preservation of modules as well as common (consensus) modules for two or more data sets. Oh, and WGCNA certainly takes expression data as input... perhaps you meant something else?