similar to: quantiles of the hypergeometric distribution (PR#502)

In both versions of R to which I currently have access (R-0.16.1 and R-0.61.1), "phyper" stops returning correct cumulative probabilities as the parameters of the hypergeometric distribution get large. For example, when N1=1345, N2=1055, and n=1330, phyper returns either 0 or 1, and nothing in between. Looking at phyper.c, it's clear what's happening. First a term (called

Hi, I hope somebody can help me on how to use the hypergeometric function. I did read through the R documentation on hypergeometric but not really sure what it means. I would like to evaluate the hypergeometric function as follows: F((2*alpha+1)/2, (2*alpha+2)/2 , alpha+1/2, betasq/etasq). I'm not sure which function should be used- either phyper or qhyper or dhyper Where

Hi Developers, The alpha, compiles successfully, but it is failing make check-all (on two seperate machines, both FreeBSD 6.1). Here is the version string: platform i386-unknown-freebsd6.1 arch i386 os freebsd6.1 system i386, freebsd6.1 status alpha major 2 minor 3.0 year 2006 month 03 day 27 svn rev

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

There is a problem with `rpois'. It does seem to take care about the order of the arguments. This is an example: > rpois(n=1,lambda=2) [1] 3 > rpois(lambda=2,n=1) [1] 2 0 It obviously uses the first argument as the number of samples to be drawn, which is wrong. I used Version 0.49 Beta (April 23, 1997). Fredrik

There is a problem with `rpois'. It does seem to take care about the order of the arguments. This is an example: > rpois(n=1,lambda=2) [1] 3 > rpois(lambda=2,n=1) [1] 2 0 It obviously uses the first argument as the number of samples to be drawn, which is wrong. I used Version 0.49 Beta (April 23, 1997). Fredrik

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:

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.:

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

(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

Dear list, I have performed several tests for the hypergeometric distribution using phyper() for some gene annotation categories as follows >phyper(26,830,31042,337, lower.tail=F) >phyper(16,387,31042,337, lower.tail=F) . . . I am only running some selected categories but I would like to correct this value for multiple testing since I have 3121 possible tests according to 3121

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

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

On a recent FreeBSD 8.0-CURRENT (i386) building R (any version) breaks with the following messages: ---------------------------------------------------------------------- [...snip...] gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -g -O2 -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include

This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---1936847065-1111238301-1101309010=:193006 Content-Type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE On Wed, 24 Nov 2004 Erik.Jorgensen@agrsci.dk wrote: > > dhyper() does not allow non-integer

Hi, set.seed(45) test1<-data.frame(columnA=rnorm(7,45),columnB=rnorm(7,10)) #used an example probably similar to your actual data apply(test1,2,function(x) sprintf("%.1f",median(x))) #columnA columnB # "44.5"? "10.2" par(mfrow=c(1,2)) lapply(test1,function(x) {b<-

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, There exists a non-central hypergeometric distribution function in the (MCMCpack) package, and a hypergeometric distribution function in the (stats) package. Is there a function for sampling from an extended hypergeometric distribution? Thanks, Narcyz This message is intended for the addressee named and may con...{{dropped}}

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

For those who are interested, I have made available a R function for noncentral hypergeometric distribution at http://www.geocities.com/jg_liao/software/Hypergeometric/hypergeometric_in_R.txt The paper that describes the algorithm will appear in The American Statistician. The function does not run on S-plus as the R's scoping rule is used. Here is how the function can be used: > n1