[R] phyper returning zero
Hi, I am attempting to use phyper to test the significance of two overlapping lists. I keep getting a zero and wondered if that was determining non-significance of my overlap or a p-value too small to calculate? overlap = 524 lista = 2784 totalpop = 54675 listb = 1296 phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=F) [1] 0 If I plug in some different values I get a p-value but since zero is actually lower is the overlap significant, or more likely have I made a mistake in using the function? phyper(10, 100, 2, 100,lower.tail = FALSE, log.p=F) [1] 2.582795e-12 Thanks Elliott This message has been scanned for malware by Websense. www.websense.com [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] phyper returning zero
On Fri, Mar 15, 2013 at 8:52 AM, elliott harrison e.harri...@epistem.co.uk wrote: Hi, I am attempting to use phyper to test the significance of two overlapping lists. I keep getting a zero and wondered if that was determining non-significance of my overlap or a p-value too small to calculate? overlap = 524 lista = 2784 totalpop = 54675 listb = 1296 phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=F) [1] 0 If you set log.p = T, you see that the _log_ of the desired value is -800, so it's likely simply too small to fit in a IEEE double. In sort, for all and any practical purposes, your p-value is zero. Cheers, MW __ R-help@r-project.org 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.
Re: [R] phyper returning zero
Thanks Michael I assumed as much but we know what that did. Thanks again. Elliott -Original Message- From: R. Michael Weylandt [mailto:michael.weyla...@gmail.com] Sent: 15 March 2013 09:29 To: elliott harrison Cc: r-help@r-project.org Subject: Re: [R] phyper returning zero On Fri, Mar 15, 2013 at 8:52 AM, elliott harrison e.harri...@epistem.co.uk wrote: Hi, I am attempting to use phyper to test the significance of two overlapping lists. I keep getting a zero and wondered if that was determining non-significance of my overlap or a p-value too small to calculate? overlap = 524 lista = 2784 totalpop = 54675 listb = 1296 phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=F) [1] 0 If you set log.p = T, you see that the _log_ of the desired value is -800, so it's likely simply too small to fit in a IEEE double. In sort, for all and any practical purposes, your p-value is zero. Cheers, MW This message has been scanned for malware by Websense. www.websense.com __ R-help@r-project.org 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.
Re: [R] phyper returning zero
eh == elliott harrison e.harri...@epistem.co.uk on Fri, 15 Mar 2013 08:52:36 + writes: eh Hi, eh I am attempting to use phyper to test the significance eh of two overlapping lists. I keep getting a zero and eh wondered if that was determining non-significance of my eh overlap or a p-value too small to calculate? well what do you guess? (:-) eh overlap = 524 eh lista = 2784 eh totalpop = 54675 eh listb = 1296 eh phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=F) eh [1] 0 Well, just *do* use log.p=TRUE : phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=TRUE) [1] -800.0408 so, indeed P = exp(-800) which is smaller than the smallest positive number in double precision, which by the way is available in R as .Machine$double.xmin [1] 2.225074e-308 I'm pretty sure that I cannot think of a situation where it is important to know that the more exact probability is around 10^(-347.45) phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=TRUE) / log(10) [1] -347.4533 rather than to know that it is very very very small. Martin eh If I plug in some different values I get a p-value but since zero is actually lower is the overlap significant, or more likely have I made a mistake in using the function? eh phyper(10, 100, 2, 100,lower.tail = FALSE, log.p=F) eh [1] 2.582795e-12 eh Thanks eh Elliott __ R-help@r-project.org 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.
