similar to: phyper returns 1 if x==k (PR#8499)

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

Dear R Users, I employed the phyper() function to estimate the likelihood that the number of genes overlapping between 2 different lists of genes is due to chance. This appears to work appropriately. Now i want to try this with 3 lists of genes which phyper() does not appear to support. Some googling suggests i can utilize the Multivariate hypergeometric distribution to achieve this. eg.:

Dear All I have a question about the hypergeomteric distribution. Example 1: I have a universe of 6187 objects, and 164 have a particular attribute, therefore 6187-164 do not have that attribute. I sample 249 of those objects, and find that 19 have that attribute. I get a p-value here (looking at just over-representation): phyper(19, 164, 6187-164, 249, lower.tail=FALSE) [1] 7.816235e-06

Dear R-users, In R 2.5.1 on Windows XP, SP2 the call to phyper(0,0,74,3,lower.tail=FALSE) returns -4.195862e-17. This does not happen with R2.5.1 on Linux, 0 is returned. Is this a bug (and should be reported as such), since phyper should not return negative values, or is this considered as one of the annoyances of finite precision arithmetic. I tend to think of this as a bug since it breaks the

Aloha all, I know too little about what I'm about to write and hope I'm not wasting your time. For a class I'm teaching in archaeological data analysis, I'm trying to put together a routine that calculates the so-called Petersen index and, especially, confidence intervals for the index. This was introduced to archaeologists by N.R.J. Fieller and A. Turner in an article

Yesterday, I installed R2.2.0 for Windows [Version 2.2.0 (2005-10-06 r35749)]. Unfortunately, 'install.packages("Matrix")' produced the following message: Warning in download.packages(pkgs, destdir = tmpd, available = available, : no package 'Matrix' at the repositories I installed lme4, maps, mapproj, CircStats, scatterplot3d, gregmisc, Hmisc without

Full_Name: Morten Welinder Version: snapshot OS: Submission from: (NULL) (65.213.85.218) Time to kick phyper's tires... The current version has very serious cancellation issues. For example, if you ask for a small right-tail you are likely to get total cancellation. For example phyper(59, 150, 150, 60, FALSE, FALSE) gives 6.372680161e-14. The right answer is dhyper(0, 150, 150, 60,

I've run into a problem with dir.create on R2.2.0 Windows XP 2002 SP 2. setwd("d:/") print(dir.create("d:\\otis-sim\\rdata", recursive=T)) print(dir.create("d:\\otis-sim\\", recursive=T)) Both return false and fail to create the directories. setwd("c:/") print(dir.create("d:\\otis-sim\\rdata", recursive=T)) Returns true and succesfully

Hello, I see the page, but there is no button to edit it. If I try to add ?action=edit to URL, wiki shows message "Nem?te dovoleno editovat tuto str?nku." (You are not allowed to edit this page). Jan ?t 3. 10. 2019 v 21:08 odes?latel David Hrb?? <david-lists at hrbac.cz> napsal: > > Jan, > > I have created the page. Are you able to edit it? > > Regards. > DH

Hello, I'm Jan Pape? and I'd like to contribute to CentOS Wiki as translator. I'm planning to translate Release Notes of CentOS 8, but now I have no rights to create new page: https://wiki.centos.org/Manuals/ReleaseNotes/CentOS8.1905/Czech My username is JanPapez. Please, could you give me an access to make it? Thank you. Jan Pape? -------------- next part -------------- An HTML

Thank you David. As it is written in article https://wiki.centos.org/Contribute#head-42b3d8e26400a106851a61aebe5c2cca54dd79e5 (Subheader 3. Contribute to the Wiki) it is necessary to write here to allow access. So I did it. Is there anybody who can give me the right to edit pages on wiki, please? Jan p? 4. 10. 2019 v 10:14 odes?latel David Hrb?? <david-lists at hrbac.cz> napsal: >

Hello, I've come across the following situation in R-1.8.1 (compile + running under RedHat 7.1): > phyper(24, 514, 5961-514, 53, lower.tail=T) [1] 1 > phyper(24, 514, 5961-514, 53, lower.tail=F) [1] -1.037310e-11 I'd expect the later to be 0 or some very small positive number. Is this a number under-flow of the calculation? Do you think I'm safe if I just set the result to 0

On 24 Nov 2003, Dirk Pape <pape@inf.fu-berlin.de> wrote: > Dear Martin Pool, > > I tried to ask via the rsync-mailing list but never got an answer. So I > contact you directly. > > I refer to the rsync syntax > > rsync [OPTION]... SRC [SRC]... DEST > > with more than one SRC, which is mentioned in the man-pages. > We use this form to "overlay"

On Fri, 4 Oct 2019 at 15:16, Alan Bartlett <ajb at elrepo.org> wrote: > > On Fri, 4 Oct 2019 at 09:37, Jan Pape? (honyczek) > <honyczek-mailing at email.cz> wrote: > > > > Thank you David. > > > > As it is written in article > > https://wiki.centos.org/Contribute#head-42b3d8e26400a106851a61aebe5c2cca54dd79e5 > > (Subheader 3. Contribute to

On Mon, 7 Oct 2019 at 06:18, Jan Pape? (honyczek) <honyczek-mailing at email.cz> wrote: > > Hi, > > it works now. Thanks Alan. > > Jan > You are welcome. Alan.

Hi all, I have tried to compute a p-value for a hypergeometric distribution as: dhyper(x,k,l,n) + phyper(x,k,l,n,lower.tail=FALSE) and sometimes obtained negative values. Do you know if it is because a round error or am I doing something wrong? Thanks in advance, Aurora

Dear R team, I have a simple question. I tried this command: phyper(17,449,19551,181, FALSE) [1] 1.47295e-07 and then I tried this command: (fisher.test(matrix(c(17,449,181,19551),2,2), alternative='greater'))$p.value [1] 3.693347e-06 Shouldn't be identical the results of the two commands ? What is the difference ? Thx a lot -- View this message in context:

Hello! I use R-version 1.0.0 To get the 0.95 quantile of the hypergeometric distribution with the parameters m=45000,n=5000 and k=600 I use the R-command > qhyper(0.95,45000,5000,600). The value obtained is 600. However, the true value is 552. The latter can be obtained for example by calling the corresponding distribution function with the R commands > x<-540:580 >

Hello, I am seeing a weird behavior from getAnalysis<>. I seem to not get back a valid object type, which leads to other errors. when I am executing the following line: InsertDummyTargsPass& dt = getAnalysis<InsertDummyTargsPass>(); I am apparently getting back an object of type llvm::Pass; This is how I checked it: with the following code I create the Object print its

(1) ...need to speed up a monte-carlo sampling...any suggestions about how I can get R to use all 8 cores of a mac pro would be most useful and very appreciated... (2) spent the last few hours trying to get pnmath to compile under os- x 10.5.4... using gcc version 4.2.1 (Apple Inc. build 5553) as downloaded from CRAN, xcode 3.0... ...xcode 3.1 installed over top of above after