[R] adjusted p value, fdr

[Ana Marija]

Thank you so much for this explanation!

On Tue, Jan 7, 2020 at 4:37 PM Yuan Chun Ding <ycding using coh.org> wrote:
>
> 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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