[BioC] p.value in eBayes( ) of limma

jihoon@cs.wisc.edu jihoon at cs.wisc.edu
Fri Jul 22 15:14:53 CEST 2005

Dear Smyth,


I'm curious about how p-value is calculated
(or which degree of freemdom is used)
from the R example of the function lm.series
in the package "limma" below.

[R Example as in help page]
M <- matrix(rnorm(100*6,sd=0.3),100,6)
M[1,1:3] <- M[1,1:3] + 2
#  Design matrix includes two treatments,
# one for first 3 and one for last 3 arrays
design <- cbind(First3Arrays=c(1,1,1,0,0,0),Last3Arrays=c(0,0,0,1,1,1))
fit <- lm.series(M,design=design)
eb <- ebayes(fit)
#  Large values of eb$t indicate differential expression

I thought following two codes should give same
results, but they didn't.
Which degree of freedom should I use to get
the same p.value?

1-pt(eb$t[1,1], fit$df[1]+eb$df.prior)

Thank you.

Jihoon Kim

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