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FDR corrected p-value on PageMan

FDR corrected p-value on PageMan
Answer
7/27/15 3:23 PM
Hi,

I am now writing a manuscript and urgently need the threshold of FDR corrected p-value that PageMan uses. I could not find this threshold although I think it must be p-value < 0.05 (the minimum number displayed on my heatmap is ~1.96). I am using multiple-hypothesis-testing correction according to false discovery rate control by Benjamini and Hochberg’s procedure (Usadel et al., 2006) for over-representation analysis.

Thanks a lot and looking very much forward your response.

Best,
Ima

RE: FDR corrected p-value on PageMan
Answer
7/28/15 12:51 PM as a reply to Ima Mulyama Zainuddin.
I truly need the answer. I really need to make sure if the minimum corrected p-value that PageMan use for Benjamini and Hochberg multiple-hypothesis-testing is p < 0.05. Because I could not find this information on PageMan analysis or probably you could show me where I can find this threshold of p-value.

Using the same analysis, I found from other paper that they mentioned p-value < 0.01. Did they set it in the beginning or is it the p-value that automatically given by PageMan? because I could not set any threshold of p-value on PageMan.

Many many many thanks in advance.

RE: FDR corrected p-value on PageMan
Answer
7/28/15 6:50 PM as a reply to Ima Mulyama Zainuddin.
From checking the code (briefly), it seems that when filtering by p-value (which is on by default) - the threshold is set to 0.05.
Is this the information you need?

RE: FDR corrected p-value on PageMan
Answer
8/13/15 11:50 AM as a reply to Marie Bolger.
Sorry just read your reply, Marie....

Yes, I finally put p-value < 0.05. Thank you :-)