similar to: phyper returning zero

Folks, It has been a whole day spent on this but I still can''t get my mind around the most probably very stupid/basic mistake here... First, the code I use: <h3>List A</h3> <ul id="lista" > <li id="item1"> Item 1</li> <li id="item2"> Item 2</li> <li id="item3"> Item 3</li> </ul>

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

Hi everybody, I am currently quite inexperienced with R. I try to create a function that simply take a value in a dataframe, look for this value in another dataframe and copy all the row that have this value This example is a simplified version of what I am doing but it's enough to help me listA Name NACE a 1 b 2 c 3 ListB NACE aaa bbb ccc 1 a a c 1 a a c 1 a a c 2 a a c 2 a a c 3 a a c 4 a

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

Full_Name: Utz J. Pape Version: 2.2.0 OS: linux Submission from: (NULL) (141.14.23.12) If I use phyper and set parameter x equal to k (meaning that all balls I draw are white) phyper returns 1 which is not (always) correct: pape at xxx:~> R2.2.0 --vanilla R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.0 (2005-10-06 r35749) ISBN 3-900051-07-0 R is free software

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.:

Hi R friends, I am posting this question even though I know that the nature of it is closer to general stats than R. Please let me know if you are aware of a list for general statistical questions: I am looking for a simple method to distinguish two groups of data in a long vector of numbers: list <- c(1,2,3,2,3,2,3,4,3,2,3,4,3,2,400,340,3,2,4,5,6,4,3,6,4,5,3) I would like to

Hi there, Given 2 lists of integer vectors, i.e.: > lista1 $"1" [1] 1 34 5 $"2" [1] 2 1 $"3" [1] 3 10 15 > lista2 $"1" [1] 1 5 $"2" [1] 2 1 $"3" [1] 3 10 29 I want to obtain the union of both, defined as the union of the vectors, that is lista.union[[1]] <- union(lista1[[1]],lista2[[1]]): > lista.union

I have 3 sortables, namely lista, listb and listc. Lista being a static list of items and will be drag n drop to listb and listc. Everytime I drag from lista to either listb or listc, the items in lista will be removed. Is that normal? If so, can anyone advice how can I maintain the items in lista so that I can have duplicate items in listb and listc. I am using rails for the development.

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,

Last night I sent the bug report below to r-help. I have since then looked at dhyper.c and found: if (NR < 0 || NB < 0 || n <= 0 || n > N) DOMAIN_ERROR; I changed 'n <= 0' to 'n < 0' and then dhyper worked as I wanted. Am I introducing some potentially dangerous behaviour by this change? Goran

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

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 >

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:

Hi, I need to run a Fisher's exact test on thousands of 2x2 contingency tables, and repeat this process several thousand times (this is a part of the permutation test for a genome-wide association study). How can I run this process most efficiently? Is there any way to optimize R code? I have my data in a 2x2xN array (N ~ 5 K; eventually N will be ~ 500 K), and use apply inside the loop:

> Dear R-users! > > I am using R 1.0.0 and Windows NT 4.0. > Suppose I have a population of N=100 subjects, a binomial variable and a random sample of n=20 subjects from my population, giving 15 "successes". I am interested in obtaining a confidence interval for the proportion of "successes" in my population. In R, I can use > library(ctest) >

Full_Name: Anja von Heydebreck Version: 1.9.1 OS: Linux Submission from: (NULL) (155.250.128.25) I obtained a negative p-value from the fisher.test() function: > fisher.test(matrix(c(14576,3023,89,68),2), alternative="g")$p.value [1] -8.426593e-13 With R 1.8.1, I got a p-value of -6.239231e-12 for this example. Anja von Heydebreck

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