Limma compare between 3 conditions vs 2 conditions

Question

[Chris]

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!

[Gordon Smyth]

Answered on Bioconductor:

• https://support.bioconductor.org/p/9157365
• https://support.bioconductor.org/p/9157606

Answer 1

[ATpoint]

Different parameters mean different estimations of model parameters etc. Things change when adding or removing groups. Decide for one strategy and go along with it. 2 vs 0 is not much different anyway in my head...

[Chris]

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.