Dear List,
   
  I've got a bit confused reading previous discussions from the list on the terminology about q values, adjusted p values and FDR in the LIMMA. Please, could you correct me if I am wrong here:
  1. BH adjusted p values from topTable or from decideTests are actually FDR. So, if we select genes with adjusted p values <0.05 then we estimate that 5% of the selected genes are not really differentially expressed, i.e. false positives.
  2. when using decideTests with method="nestedF", p.value =0.01 and adjust.method="BH", does it give you the list of genes for which BH adjusted F.p values <0.01, so one should expect 1% of false positive results in the list of the selected genes?
   
  With kind regards,
  Lev.

       
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