[BioC] mt.teststat

[w.huber at dkfz-heidelberg.de]

On Tue, 8 Apr 2003, Park, Richard wrote:
> I was wondering if anyone could interpret the raw p-values calculated
> using mt.teststat() (this function is part of the multtest package). I
> am using the following lines:
>
> teststat <- mt.teststat(compSet, label, test="t", nonpara="n")
> rawp <- 2 * (1-pnorm(abs(teststat)))


Hi Richard,

mt.teststat is fine. You need to use the "pt" function and not "pnorm" if
you want to calculate the p-value of a t-test from the t-statistic. Also,
in order to compare it to the result of ctest::t.test, there you'll have
to use var.equal=TRUE.

Best regards
Wolfgang