[BioC] Storey and Tibshirani FDR

[Naira Naouar]

Hi Daniel,

You could use the Qvalue package in R to implement the Storey and 
Tibshirani's approach.
Benjamini and Hochberg's method is a special case of the Storey and 
Tibsirani's that you can apply with the qvalue function by fixing lambda 
to 0.

Example of use:
## p is the vector containing the pvalues to correct for multiple testing

 >library(qvalue)
 >qobj = qvalue(p)   ## will return an object containing the corrected 
pvalues with the default Storey and Tibsirani's approach.
 >qobj$qvalue     ## is the vector containing the corrected pvalues = qvalue

 >qobj = qvalue(p,lambda=0)  ## will return an object containing the 
corrected pvalues according to Benjamini and Hochberg

Hope this helps,
Naira

Daniel Brewer wrote:
> I am trying to recreate some results from an external microarray dataset
> and they use Storey and Tibshirani's False Discovery Rate for multiple
> testing correction.  Is this implemented in Bioconductor at all?  Having
> a quick glance at the paper it looks like it is related to Benjamin
> Hochberg but not quite the same.
>
> Thanks
>
>   


-- 
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Naira Naouar 

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VIB Department of Plant Systems Biology, Ghent University
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