Hi Tim,

Thank you very much for your reply. So BH(95) method is the most general
FDR-controlling method which can be applied to the case for small number of
testes, right?

Feng

On Wed, Jul 3, 2013 at 5:59 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote:

> qvalues are not appropriate for an experiment where there is such a small
> number of tests.
>
> To compute q-values, the proportion of true nulls must be estimated, which
> requires enough data points (i.e., enough tests being done) to estimate the
> parameters of a two-component mixture model.  I dimly recall the lower
> bound for such an estimate to be any good is around 3000 tests, and more is
> better.
>
> Furthermore, the estimate (mentioned above) is then simply applied to the
> B&H-corrected pvalues.
>
> So:
>
> p.adjust(your.p.values, method='fdr')
>
> is probably the most sensible choice for your experiment.
>
> Hope this helps,
>
> --t
>
>
>
> On Wed, Jul 3, 2013 at 1:55 PM, Feng Tian <fengtian@bu.edu> wrote:
>
>> Hi Dear all,
>>
>> I need to do multiple testing correction for my results which contains
>> about 200 tests. I find that there are two general methods to do FDR
>> controlling. One is the BH method and the other one is the Storey
>> (q-value). The results from two methods are quite different. Usually,
>> Storey method can get more significant results than BH method. So which I
>> should I use? Are there some guildlines for choosing appropriate method to
>> do FDR controlling?
>>
>> Thanks and have a nice day.
>>
>> Feng
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>

	[[alternative HTML version deleted]]

