[BioC] How to get adjusted p values after "global" fdr correction in decideTests (limma)

[Paolo Innocenti]

That works!

Thank you,
paolo


Gordon K Smyth wrote:
> Dear Paolo,
> 
> What you say is correct.  The only way to get the adjusted p-values to 
> go with method="global" is
> 
>   adj.p <- p.adjust(fit$p.value, method="BH")
> 
> where 'fit' is the fit object that you gave to decideTests().
> 
> Best wishes
> Gordon
> 
>> Date: Wed, 23 Jul 2008 12:24:43 +0200
>> From: Paolo Innocenti <paolo.innocenti at ebc.uu.se>
>> Subject: [BioC] How to get adjusted p values after "global" fdr
>>     correction in decideTests (limma)
>> To: AAA - Bioconductor <bioconductor at stat.math.ethz.ch>
>>
>> Hi all,
>>
>> I used the option "global" in decideTests(), in order to correct for FDR
>>  taking into account my 3 contrasts simultaneously.
>>
>> The list of DE genes I got is longer than the one I get using "separate"
>> option (and this should be ok, see here):
>> http://thread.gmane.org/gmane.science.biology.informatics.conductor/17847
>>
>> Now, topTable and write.fit implement FDR adjustment with method
>> "separate", so if I extract the p.values from these objects, some of
>> them, in my situation, will be inevitably higher than 0.05.
>>
>> How can I get the correct p.values?
>> Am I missing something obvious?
>>
>> Thanks in advance for any hints,
>> paolo
>>
>>
>>
>> -- 
>> Paolo Innocenti
>> Department of Animal Ecology, EBC
>> Uppsala University
>> Norbyv?gen 18D
>> 75236 Uppsala, Sweden
> 
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-- 
Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyvägen 18D
75236 Uppsala, Sweden