[BioC] EdgeR: about FDR

[Gordon K Smyth]

Anna,

I found your question difficult to interpret.

If I understand your question correctly, you have compared a treatment A 
back to a control treatment, and you have also compared treatment B back 
to the control.  So you have contrasts AvsControl and BvsControl.

Now you make the contrast BvsControl-AvsControl, and you find some genes 
significant that were not significant for either BvsControl or AvsControl.

This is not a mistake, and it's no great mystery.  It can easily be that B 
is higher than the Control for some gene, but not by enough to reach 
signficance, and A is less the control for the same gene, but not by 
enough to reach significance, but the combined difference B vs A is large 
enough to be significantly greater than zero.  This is just because B-A is 
larger than either B-Control or A-Control.  In such cases, you know that A 
and B are different, but it is not necessarily discernible whether both or 
just one are different from the control.

How you interpret such genes depends on your scientific questions.  We 
can't tell you how to do that.

Best wishes
Gordon

PS. Please check over the posting guide, which has been expanded recently:

   http://www.bioconductor.org/help/mailing-list/posting-guide/


--------- original message --------
[BioC] EdgeR: about FDR
anna [guest] guest at bioconductor.org
Sat Nov 3 14:22:38 CET 2012

Hello dear List,
I conducted an analysis with EdgeR and I thank you for this software.
I have a list of DE genes after treatment A and one after treatment B.
using the cntrast fucntion, I also have the comparison of A and B, which 
shows 43 differentially regulated genes. When I check FDR and logFC fot 
those 43 genes, they are signicant.
But when I come back to list A or B,
I see that some of those 43 genes did not reach significance either for 
FDR or for logFC, in either list A or B.
Should I then get rid of those genes,
or FDR in the contrast output takes that into account ?
thanks a lot for you answers,
best regards,
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


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