[R] adjusted p value, fdr

[Yuan Chun Ding]

When you do x1g$fdr, you adjusted for  a total of 15568  tests, so FDR is high for those first four entries. When you do p.adjust(pval,method="BH"), you assumed there were only a total of 4 multiple tests in your experiment, so FDR is low.

Ding

-----Original Message-----
From: R-help [mailto:r-help-bounces using r-project.org] On Behalf Of Ana Marija
Sent: Tuesday, January 07, 2020 2:18 PM
To: r-help
Subject: [R] adjusted p value, fdr

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Hello,



I have a data set which has 15568 entries



I am trying to calculate adjusted p values using p value via:



head(x1g)



                                                   t      P.Value

      adj.P.Val          B       fdr

3TXADqtSkhV1IXRHlg  4.468671 3.072189e-05 0.4782784  1.5253151 0.4782784

34lG83aZ6.WLFnge6s  4.217037 7.518696e-05 0.5852553  0.8660534 0.5852553

oS67lguv5HpU4i6Pvg -3.939182 1.959413e-04 0.9994637  0.1600655 0.9994637

Qpc2sX7gp.W5E2rRS4  3.732914 3.900822e-04 0.9994637 -0.3471331 0.9994637

NqsVOy_yos30cOQRSE -3.673551 4.737810e-04 0.9994637 -0.4902001 0.9994637

B3SDpegGjpdxnvU0S0 -3.665765 4.859528e-04 0.9994637 -0.5088638 0.9994637



x1g$fdr=p.adjust(x1g$P.Value,method="BH")



the fdr values seem unusually high



if I just do it for the first few p values from my x1g data frame:

>pval=c(3.072189e-05,7.518696e-05,1.959413e-04,3.900822e-04)

> p.adjust(pval,method="BH")

[1] 0.0001228876 0.0001503739 0.0002612551 0.0003900822



Can someone please explain what might be the issue.



Thanks

Ana



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