Dear James, Guido and Bioconductor helpers,
I always thought, q-values control pFDR, which is similar to FDR almost all
the time but theoretically not similar.

Please correct me if I am wrong.

Thanks and Best Regards,
Sanvesh

On Wed, Feb 3, 2010 at 5:14 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote:

> Hi Guido,
>
>
> Guido Leoni wrote:
>
>> Dear List
>> I'm new to microarrays analysis. I'm analyzing an experiment with 2
>> condtions and 3 microarrays for condition. My data are succesfully
>> normalized and I have a list of gene modulated with aFC, a raw p-value and
>> a
>> q-value. My q-value are never lower than 0,1. If I well understand my
>> q-value is the minimum false discovery rate for which my FC are
>> statistically significant. So have I set a threshold similar to p-value to
>> select my differentially regulated genes? if yes (what does mean the fact
>> that my q-value is never lower than 0,1?)
>> Sorry for my confused question and
>> Thank you for every tips you could give to me
>>
>
> The FDR is an estimate of the maximum percentage of 'significant' results
> that are false positives. So for instance, if you accept all the genes
> (reporters) with a q-value =< 0.1, then the assumption is that somewhere
> around 10% of those are false positives.
>
> So when you go to validate those genes (if you use that FDR level), you can
> expect about 10% or so to fail to validate. This of course assumes that all
> the assumptions have been met blah blah statistics statistics statistics...
> ;-D
>
> Best,
>
> Jim
>
>
>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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> 1241 E. Catherine St.
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> 734-615-7826
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