[BioC] Limma FDR and p.value

[Saurin Jani]

Hi,

This might be simple question, but I am confused
somehow..if anyone can guide me through this that
would be great.


> fit<- eBayes(fit);

> results_fdr1<- classifyTestsP(fit, p.value=0.01, 
  method="fdr")

> vennDiagram(results_fdr1,include = "both");
  (I get very nice vennDiagram, my all contrasts have 
   nice numbers of genes)

> coef1_Genes <- topTable(fit,coef = 1, adjust = 
  "fdr",number = 50); 

Above when I get coef1_Genes, which has adjusted
P.value way higher than 0.01, sometimes its range from
0.5.....0.904 or something like that. so, how can I
decide my cutoff for FDR? I saw nice numbers in my
vennDiagram above so, i thought I have lots of genes
which has < 0.01 FDR but it not when I checked in
coef1_Genes. 

In above results coef1_Genes P.value = FDR cutoff
right? There is no option in topTable for howmuch FDR
level..!

I set p.value = 0.01 in classifyTestsP function so, I
think classifyTestsP gives me FDR level < 0.01,
because I am using method = "fdr", and those nice
number I see in vennDiagram.......Is this right
understanding? if yes then how can I access those
genes? 


Please, let me know, I highly appreciate your help in
advance.

Thank you,
Saurin

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Saurin's WebWorld: http://hawkmail.monmouth.edu/~s0451884