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Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k

I don't think that your scientific reasoning here is correct. If there is no DE at the gene level, then it is also very unlikely that there…

Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
•
0

Thanks Gordon! I really appreciate your help! Maybe I don't know how to make the right effort which make me go back and forth. Just keep tr…

Answer: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k

Everyone has advised you to use limma. The reason why limma is recommended over just running t.test() or lm() or aov() row by row is becaus…

Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k

Yes, it is important that you feed all the pathways into limma, so that limma can robustly estimate the variances, even if you only going t…

Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
•
0

Thanks Robert! Please correct me if I am wrong, so using more pathways (feeding more data in limma) gives us more accurate raw p value?

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