[BioC] Limma and negative p-values

[Ovokeraye Achinike-Oduaran]

Thanks Steve and Naomi.

-Avoks

On 15 Mar 2012, at 5:37 PM, Naomi Altman <naomi at stat.psu.edu> wrote:

> I have posted this several times, but it has been a while so I will do it again.
> 
> Suppose p=.001 and you have 10000 genes.  Then you expect 10 significant genes just by chance.  So if you observe 9 or 10 significant genes at this level, your FDR should be 100%.  If you observe 11, your FDR should be about 10/11=0.91.  Etc.
> 
> This does not mean that you don't have any significant genes.  It means your experiment did not have enough power to detect them.
> 
> --Naomi
> 
> 
> At 10:31 AM 3/15/2012, Ovokeraye Achinike-Oduaran wrote:
>> Hi,
>> 
>> Excuse the language but I say shady because they all range from ~0.918 - 0.999.
>> 
>> On Thu, Mar 15, 2012 at 3:54 PM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com> wrote:
>> > Hi,
>> >
>> > On Thu, Mar 15, 2012 at 9:50 AM, Ovokeraye Achinike-Oduaran
>> > <ovokeraye at gmail.com> wrote:
>> >> Hi all,
>> >>
>> >> Sorry...a recall of my previous mail...the p-values are fine(or not)
>> >> but not negative...the corrected p-values, however, look very shady.
>> >> Any suggestions there?
>> >
>> > Shady?
>> >
>> > Need to elaborate, please.
>> >
>> > -steve
>> > --
>> > Steve Lianoglou
>> > Graduate Student: Computational Systems Biology
>> >  | Memorial Sloan-Kettering Cancer Center
>> >  | Weill Medical College of Cornell University
>> > Contact Info: http://cbio.mskcc.org/~lianos/contact
>> 
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> 
> 
>