Thank you so much for your reply. In each condition (normal, early state, late state), I have multiple samples. I mean when I compare normal vs early vs late state, there is no significantly different but when I compare normal vs late state, there are pathway score significantly different.
Limma compare between 3 conditions vs 2 conditions
Hi Biostar,
When I compare pathway score between 3 conditions, I have no pathway score significantly different ( p value < 0.05). But when I exclude one condition, there are 2 pathway score significantly different. May I know why? The output from topTable also changes when we no longer pairwise compare. Thank you so much!
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Gordon Smyth
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Chris •
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