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Dear List,
Sorry to bring up this adjusted p value question about limma. I
searched mail
list but didn't find an answer.
I know limma use "p.adjust()" for multiple test correction. And if
there is only
one coefficent, the adjust p values results of limma's top table is
the same as
I directly apply p.adjust to the P.Value vector.
My question is that if we have several coefficent, for example, 3
comparisons,
how does limma use the p.adjust()?
I tried to feed p.adjust() as: p.adjust(tp$P.Value,
method="fdr",n=length(tp$P.Value) * 3), but the results are different
from the
tp$adj.P.Val.
Could some let me know how limma apply p.adjust() to handle this
situation
(several comparisons/coefficents)?
Thank you.
Regards,
Xiaokuan
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