Thank you so much for this explanation! On Tue, Jan 7, 2020 at 4:37 PM Yuan Chun Ding <ycd...@coh.org> wrote: > > When you do x1g$fdr, you adjusted for a total of 15568 tests, so FDR is > high for those first four entries. When you do p.adjust(pval,method="BH"), > you assumed there were only a total of 4 multiple tests in your experiment, > so FDR is low. > > Ding > > -----Original Message----- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Ana Marija > Sent: Tuesday, January 07, 2020 2:18 PM > To: r-help > Subject: [R] adjusted p value, fdr > > [Attention: This email came from an external source. Do not open attachments > or click on links from unknown senders or unexpected emails.] > > ---------------------------------------------------------------------- > Hello, > > > > I have a data set which has 15568 entries > > > > I am trying to calculate adjusted p values using p value via: > > > > head(x1g) > > > > t P.Value > > adj.P.Val B fdr > > 3TXADqtSkhV1IXRHlg 4.468671 3.072189e-05 0.4782784 1.5253151 0.4782784 > > 34lG83aZ6.WLFnge6s 4.217037 7.518696e-05 0.5852553 0.8660534 0.5852553 > > oS67lguv5HpU4i6Pvg -3.939182 1.959413e-04 0.9994637 0.1600655 0.9994637 > > Qpc2sX7gp.W5E2rRS4 3.732914 3.900822e-04 0.9994637 -0.3471331 0.9994637 > > NqsVOy_yos30cOQRSE -3.673551 4.737810e-04 0.9994637 -0.4902001 0.9994637 > > B3SDpegGjpdxnvU0S0 -3.665765 4.859528e-04 0.9994637 -0.5088638 0.9994637 > > > > x1g$fdr=p.adjust(x1g$P.Value,method="BH") > > > > the fdr values seem unusually high > > > > if I just do it for the first few p values from my x1g data frame: > > >pval=c(3.072189e-05,7.518696e-05,1.959413e-04,3.900822e-04) > > > p.adjust(pval,method="BH") > > [1] 0.0001228876 0.0001503739 0.0002612551 0.0003900822 > > > > Can someone please explain what might be the issue. > > > > Thanks > > Ana > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!Fou38LsQmgU!4bosaaipAoQGBWeAiIEWMDxU4RRjSCsN0DmyN4DzNZK1NSLhh5pdAGPEy5zh$ > > PLEASE do read the posting guide > https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!4bosaaipAoQGBWeAiIEWMDxU4RRjSCsN0DmyN4DzNZK1NSLhh5pdADDOUx9a$ > > and provide commented, minimal, self-contained, reproducible code. > > ---------------------------------------------------------------------- > ------------------------------------------------------------ > -SECURITY/CONFIDENTIALITY WARNING- > > This message and any attachments are intended solely for the individual or > entity to which they are addressed. This communication may contain > information that is privileged, confidential, or exempt from disclosure under > applicable law (e.g., personal health information, research data, financial > information). Because this e-mail has been sent without encryption, > individuals other than the intended recipient may be able to view the > information, forward it to others or tamper with the information without the > knowledge or consent of the sender. If you are not the intended recipient, or > the employee or person responsible for delivering the message to the intended > recipient, any dissemination, distribution or copying of the communication is > strictly prohibited. If you received the communication in error, please > notify the sender immediately by replying to this message and deleting the > message and any accompanying files from your system. If, due to the security > risks, you do not wish to r eceive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) > ------------------------------------------------------------
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