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Old 11-12-2013, 07:00 AM   #1
Location: IL

Join Date: May 2011
Posts: 71
Default How to adjust the p values of edgeR?

Hi every one,

I am trying adjust the p values of my two-treatment comparison by edgeR. I am not sure if FDR need to be calculated with topTags before the adjustion, because exactTest just gives the p values without FDR.

In addition, how can I extract the DE genes with padjusted <= 0.05 from the following dataframe.

logFC logCPM PValue FDR padjusted
GB49890-RA 5.557823 7.1075888 1.018805e-43 1.978520e-40 1.978520e-40
GB46236-RA 4.667221 0.7197219 7.988596e-19 5.921318e-17 5.921318e-17
GB52184-RA 4.516693 1.3326365 1.519341e-23 2.269662e-21 2.269662e-21
GB50109-RA 4.477469 3.9928677 3.167978e-07 2.177004e-06 2.177004e-06
GB48922-RA -4.305247 2.7841370 4.546438e-29 2.006632e-26 2.006632e-26
GB40248-RA 4.127615 7.1749037 9.026131e-28 3.130133e-25 3.130133e-25

Thanks a lot!!

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