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

Michal Blazejczyk michal.blazejczyk at mail.mcgill.ca
Mon May 4 18:41:02 CEST 2009

Hi Holger,

Thank you for the answer!

I've got one more small question: is the FDR algorithm used in SAM
like one of the commonly known DFS's (Bonferroni, Benjamini-Hochberg,
Sidak), or is it a special FDR developed for SAM?

Best regards,
Michal Blazejczyk

Holger Schwender <holger.schw at gmx.de> wrote:
> If you are okay with the assumption that all genes follow the same null
> distribution (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.

> Holger

> -------- 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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