Question: F-tests for factorial effects - limma

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Naomi Altman •

**6.0k**wrote:I am analyzing a 2-factor factorial Affy experiment, with 3 d.f. for
each
factor.
I would like to get the F-tests for the main effects and interactions
using
limma.
I have computed all the contrasts, and got the t-tests (both
unadjusted and
eBayes). I do know how to combine these into F-tests "by hand" but I
could
not figure out if there was a simple way to do this using limma.
I had a look at FStat (classifyTestsF). There seems to be a problem,
in
that the matrix tstat is not premultiplied by the contrast matrix when
the
F-statistics are computed. So, if the contrasts are not full-rank, an
error is generated (instead of the F-statistics) because nrow(Q) !=
ncol(tstat).. (See the lines below).
if (fstat.only) {
fstat <- drop((tstat%*% Q)^2 %*% array(1, c(r, 1)))
attr(fstat, "df1") <- r
attr(fstat, "df2") <- df
return(fstat)
}
I figured that before I fiddled with the code, I would check to make
sure
that I didn't miss an existing routine to do this.
Thanks in advance.
Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348
(Statistics)
University Park, PA 16802-2111

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modified 14.5 years ago
by
Gordon Smyth ♦

**37k**• written 14.5 years ago by Naomi Altman •**6.0k**