[BioC] EdgeR: about FDR

[anna [guest]]

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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