I have microarray data from two experiments that differ in the type of tissue that the RNA was extracted from. In both experiments, tissue was infected with a virus or mock-infected (paired within donors) and we looked for probes that were DE between virus and mock. I am interested in which DE probes were found in both experiments (tissue types) and which were exclusive to one or the other.
Things that were the same in both microarrays: virus and dose, lumi/limma analysis and cut-offs, platform
Things that were different: Tissue type (cells vs. tissue explants), tissue donors, # of donors,
I think this is basically like a single experiment with the tissue type totally confounded with the fact that the different types were run on different arrays and donor confounded with tissue type.
Question: If I just want to look at which DE probes overlap, do I need to combine the data set and anaylze as for a meta-analysis using GeneMeta or similar, or, can I simply compare the probes?
Many thanks in advance,
University of Washington
Hladik Lab UW-OB/GYN BB630
Fred Hutchinson Cancer Research Center VIDD Affiliate