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Old 01-27-2014, 03:34 AM   #11
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Location: Norway

Join Date: Aug 2013
Posts: 266

"make an informed case-by-case decision what FDR might be acceptable for a given experiment"

Could you please elaborate?

How about this case:

You run DESeq2, you pick out 10 genes you want to look at including p values.
Say 6 genes have p < 0.05.
You then use p.adjust in R.
What FDR do you choose and why?
Which n do you set?

Last edited by sindrle; 01-27-2014 at 05:03 AM.
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