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

Comment: Why p value inconsistent when using different number of pathway score?
by
Robert Castelo
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3.2k

It seems that you are thinking that when you look at the results of limma for a particular gene, or pathway if you want, those results were…

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

Thanks ATpoint for you advice. Just don't understand the math behind the change in raw p value in this case. I think it is important to und…

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