Hi Tom, >From a quick scan of the docs, I think you are looking for qobj$pi0. The vector qobj$qvalue seems to be the local false discovery rate for each of your randomizations. Note that the manual implies that the p values are those of multiple comparisons within a data set, not randomizations of the data, so I'm not sure that your usage is valid for the function..
Jim On Fri, Jan 13, 2017 at 4:12 AM, Thomas Ryan <tombernardr...@gmail.com> wrote: > Hi all, I'm wondering if someone could put me on the right path to using > the "qvalue" package correctly. > > I have an original p value from an analysis, and I've done 1,000 > randomisations of the data set. So I now have an original P value and 1,000 > random p values. I want to work out the false discovery rate (FDR) (Q; as > described by Storey and Tibshriani in 2003) for my original p value, > defined as the number of expected false positives over the number of > significant results for my original P value. > > So, for my original P value, I want one Q value, that has been calculated > as described above based on the 1,000 random p values. > > I wrote this code: > > pvals <- c(list_of_p_values_obtained_from_randomisations) > qobj <-qvalue(p=pvals) > r_output1 <- qobj$pvalue > r_output2 <- qobj$qvalue > > r_output1 is the list of 1,000 p values that I put in, and r_output2 is a q > value for each of those p values (i.e. so there are 1,000 q values). > > The problem is I don't want there to be 1,000 Q values (i.e one for each > random p value). The Q value should be the false discovery rate (FDR) (Q), > defined as the number of expected false positives over the number of > significant results. So I want one Q value for my original P value, and to > calculate that one Q value using the 1,000 random P values I have generated. > > Could someone please tell me where I'm going wrong. > > Thanks > Tom > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. ______________________________________________ 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.
