[BioC] SAM results

[Holger Schwender]

Hi Michal,

the d-values are the values of the moderated t-statistic (called d-statistic in the Tusher paper about SAM). The q-values are the FDR adjusted p-values as proposed by John Storey. And so yes, you can (and actually should if you wanna use them) adjust the raw p-values with any multiple correction procedure. The only difference of these p-values (when computed permutation-based) to other permutation-based p-values is that the p-values in SAM are computed based on all mB permuted values for the m genes and B permutations, while the usually used p-values are determined on the B gene-specific permutations.

Best,
Holger 



-------- Original-Nachricht --------
> Datum: Wed, 10 Nov 2010 13:25:27 -0500
> Von: Michal Blazejczyk <michal.blazejczyk at mail.mcgill.ca>
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC] SAM results

> Dear List,
> 
> I have a question regarding p-values, d-values and q-values returned
> by Bioconductor's SAM method (siggenes package).
> 
>  - My understanding is that the p-values returned are unadjusted.
>    Does it make sense to apply standard FDR procedres (e.g. Benjamini-
>    Hochberg) to them?
> 
>  - What is the definition of d-values and q-values?
> 
> Best,
> Michal Blazejczyk
> 
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