alex lam (RI) wrote: > Dear colleagues, > > This is not strictly a R question, but I hope it is ok to ask on the > list. > I fed a vector of p-values from about 20 million anova tests to the > package q-value and obtained this output: > >> qsummary(asso_p.qvalue) > > Call: > qvalue(p = asso_p.vec) > > pi0: 1 > > Cumulative number of significant calls: > > <1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1 > p-value 22711 59067 262103 551316 1013241 1936797 20048103 > q-value 3554 5211 9275 12807 16951 24557 20048103 > > I can see that there are many hits with very small q-values ,say q > <0.001, so to use that as cut off I have 5211 significant hits and can > expect ~ 5 false postives. But my pi0 is 1. Does it mean that all my > tests are true null and there are no significant results?
Well, yes, at least under H0 you would expect the above results in such a case. Concluding without further information that *all* are non-significant is impossible, though. This requires some interpretation depending on where the tests some from... Uwe Ligges > Thanks for your help. > Alex > > ------------------------------------ > Alex Lam > PhD student > Department of Genetics and Genomics > Roslin Institute (Edinburgh) > Roslin > Midlothian EH25 9PS > > Phone +44 131 5274471 > Web http://www.roslin.ac.uk > > ______________________________________________ > [email protected] mailing list > 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. ______________________________________________ [email protected] mailing list 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.
