Another question about LIMMA. I performed experiments with Illumina platform and there are around 45000 probes for the whole genome. I want to compare a drug treatment. When I used Limma module, and iinput normalized results from all the probes, I could not get any significant genes out. But if I only used the genes with significant detection values (Then I ended up around 18000 genes), I got several hundreds significant genes. I wonder which result I should trust. I do not know much about the math behind LIMMA. But is that because the genes with non significant detections ( so with lower and more variable signals) will affect the multiple testing dramaticly?
Thanks a lot!
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