Hi All,

I have used limma to analyze the time course microarray data (ctrl, 3Hr,
12Hr and 24Hr; each having 3 arrays). Using eBayes(), I have calculated
F.p.value and it's corresponding FDR using p.adjust. I also used
'decideTests(fit1, method="nestedF", adjust.method="BH")'.
Now I can choose probesets based on FDR calculated by p.adjust or by using
results given by 'nestedF'. I can clearly see that the number of significant
probesets given by 'nestedF' is larger than by 'FDR calculated by p.adjust'
at the same cutoff value 0.05. Which one is the preferred method for
choosing significant probesets?

Your suggestions are greatly appreciated.

Thanks,
Sharon

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