[BioC] EdgeR: about FDR

[James W. MacDonald]

Hi Anna,

On 11/3/2012 10:23 AM, anna [guest] wrote:
> hi again everybody,
> actually log FC is not a worry because I can choose a cut-off myself ( logFC>1 for example),
> the worry is more about FDR that are>0.05 in list A or B, but still the gene has FDR<0.05 in the contrast list,
> so is that gene significantly differently regulated ?

If I understand what you have done, you are asking three different 
questions:

Is a gene differentially expressed after treatment A
Is a gene differentially expressed after treatment B
Is a gene differentially expressed when comparing treatment A to treatment B

So if I assume that questions 1 & 2 are treatment/control, and question 
3 is treatment A/treatment B, then there are several scenarios where 1 & 
2 wouldn't be significant, but 3 would. For instance:

Gene x goes down in treatment A vs control, but not significantly.
Gene x goes up in treatment B vs control, but not significantly.
Gene x is significantly different between treatment A and treatment B, 
because the gene goes in different directions in each treatment, and 
when comparing the treatments this difference is large enough to be 
significant.

Best,

Jim


> thanks,
> anna
>
>   -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099