[BioC] retrieving specific FDR value from SAM

[Holger Schwender]

Hi,

with the current release version (1.10.1) of siggenes, you have to try several delta values to find the delta value that leads to a specific FDR. However, I have currently implemented a function called findDelta which is available in siggenes 1.11.10 and later (you can download this version from the developmental branch of Bioconductor) that exactly does what you want: E.g.,

> findDelta(sam.out, 0.2)

gives you the delta value and the number of genes called significant if the FDR should be 0.2.

Best,
Holger


-------- Original-Nachricht --------
Datum: Tue, 24 Jul 2007 11:50:57 -0400
Von: "Alex Tsoi" <tsoi.teen at gmail.com>
An: bioconductor at stat.math.ethz.ch
Betreff: [BioC] retrieving specific FDR value from SAM

> Dear all,
> 
> 
> I am working on a meta microarray analysis, and I have + 10 SAM output
> (the
> sam() results). For each of the output, I would like to get the delta
> value
> that is corresponding to a specific FDR (eg. 0.2), and use the delta value
> to get the summary of the sam for retrieveing the differentially expressed
> genes. Could any of you show me how to automatically get the delta value
> that is corresponding to a specific FDR ?
> 
> Many thanks
> 
> -- 
> Lam C. Tsoi (Alex)
> Medical University of South Carolina
> 
> 	[[alternative HTML version deleted]]
> 
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