[BioC] P-values returned from siggenes's sam() function

Holger Schwender holger.schw at gmx.de
Sun May 3 05:26:53 CEST 2009

If you are okay with the assumption that all genes follow the same null disrtibution (and I guess so, as you are using sam), then yes.

In fact, these raw p-values are used to compute the q-values (result at q.value), i.e. FDR adjusted p-values.


-------- Original-Nachricht --------
> Datum: Thu, 30 Apr 2009 13:45:25 -0400
> Von: Michal Blazejczyk <michal.blazejczyk at mail.mcgill.ca>
> An: bioconductor at stat.math.ethz.ch
> CC: Holger Schwender <holger.schw at gmx.de>
> Betreff: P-values returned from siggenes\'s sam() function

> Hi everyone,
> I have a fairly technical question.  We are calling the sam() function
> from packages siggenes:
>   result <- sam( ...... )
> and then getting the p-values like this:
>   result at p.value
> The Help for function sam() says that these are "raw, unadjusted p-values
> of the genes".
> Does it mean an FDR function such as mt.rawp2adjp() from multtest can be
> safely used on these values?
> Best,
> Michal Blazejczyk
> FlexArray Lead Developer


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