On Oct 1, 2013, at 3:16 AM, Smeeta shrestha wrote: > Dear Dr Friedman, > > I am keen to know the cut off for Adjusted- pvalue . I saw your post to Delasa.(I have attached the whole post in this email for your reference) > > "Say you use a p-value cutoff <0.05. As long as this value is not exceeded it is reasonable to take p-adjust (fdr) at 0.1 or even as high as 0.5 as long as you know that in the latter case have the genes you try to validate by pcr are expected not to be differentially expressed. I think that p-adjust<0.05-0.25 are good cutoffs". > > I would like to know is there any material which explains or justifies the reason behide how much fdr cut off I can take. > > My data with p value 0.05 shows a huge set of genes. But when corrected using Benjamini Hochberg correction. I get no genes on adjusted pvalue cut off of 0.05. The closest i get is 0.556. > > Please any input would be most helpful. > > Thank you for your attention. > > sincerely > Smeeta Shrestha > Post doctoral Fellow > CCMB > Hyderabad > India. > <fdr.docx> Dear Smeeta, First of all, it is best to copy the list in all queries. I know of know specific reference and indeed I ventured above fdr<0.05 based on a conversation with Terry Speed (and I hope that I am not misquoting or misinterpreting) in which he said that the fdr cutoff "depends upon what you use the data for". This makes sense, in that the fdr is the number of statistically significant genes by the rawp<0.05 criterion that are likely to be false. So fdr = 0.556 means that the Benjamini-Hochberg fdr predicts that there is a 56% chance that your most signficant gene really is not significant. So it will be a bad bet to expect this gene to be validated by pcr, I would be interested in what other correspondents have to say in this matter. Best wishes, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet)/ Columbia Department of Systems Biology Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "You shouldn't have told Isaac to say 'hi' to Snowden when he's at the Moscow airport. He will do it and then he won't be able to get a computer job." - Judith Friedman, Age withheld on request