For limma, if I leave coef=NULL, which test is the P value for?
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@0b4d0d5b
Last seen 5 months ago
Norway

As the subject line says, what does the P value of limma with coef=NULL for topTable indicate?

limma • 441 views
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ATpoint ★ 4.0k
@atpoint-13662
Last seen 2 days ago
Germany

It does an ANOVA-like F-test using all coefficients, so basically testing for any difference across the set of groups in the design.

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@gordon-smyth
Last seen 5 hours ago
WEHI, Melbourne, Australia

If you type help(topTable), the help page says:

If coef is left NULL, then all the coefficients or contrasts in the fitted model are used, except that any coefficient named (Intercept) will be removed.

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