[BioC] Question: limma decideTests nestedF p-values

[Gordon K Smyth]

No, there is no way to get individual p-values corresponding to the nestedF method.  You can
however just used the overall F-test p-values, fit$F.p.value, which will give you p-values at the
probe level rather than the contrast level.  Use

  p.adjust(fit$F.p.value)

to get adjusted p-values.  The nestedF method will give at least one significant contrast for a
given probe if and only if the above adjusted p-value is less than the cutoff.

Best wishes
Gordon

> Date: Thu, 16 Feb 2006 17:17:08 +0100
> From: Georg Otto <georg.otto at tuebingen.mpg.de>
> Subject: [BioC] Question: limma decideTests nestedF p-values
> To: bioconductor at stat.math.ethz.ch
>
> Hi!
>
> I am using decideTests with the method "nestedF" to get differentially
> expressed genes. My question is: how can I use nestedF (or
> heirarchical) to get the actual adjusted p-values (instead of -1,0,1)?
>
> Best,
>
> Georg