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

[jihoon@cs.wisc.edu]

Dear Smyth,

Hello,

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$t indicate differential expression
qqt(eb$t[,1],df=fit$df+eb$df.prior)
abline(0,1)



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?


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



Thank you.


Jihoon Kim