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 receive 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) ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
