similar to: Multiple testing corrections on very large vector

Hello R experts, I am trying to analyze this dataset and am stuck on this problem for quite some time now. I am using mt.rawp2adjp. the output that came out was a matrix with two colums since I had asked it to calculate the adjusted p values using one method. so it has the two columns as: rawp BH I combined these using cbind with my actual dataframe. checked using head all was fine. thereafter I

> dim(data.sub) [1] 10000 140 #####extracting all differentially express genes########## library(multtest) two_side<- (1-pt(abs(data.sub),50))*2 diff<- mt.rawp2adjp(two_side) all_differ<-diff[[1]][37211:10000,] all_differ #####list of differentially expressed genes########## > probe.names<- + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] Error in

Hi R users I try to use the lme but I can?t!!!!! My script is (some words in french, sorry!!): rm(list=ls(all=TRUE)) #Efface tous les objets en m?moire pour ?viter des erreurs library(MASS) #Chargement des Librairies library(car) library(Hmisc) library(tkWidgets) library(svDialogs) library(multtest) library(nlme) #Rep <- "C:/Documents and Settings/U3M/Bureau/steph/Scripts

Hola a todos, Tengo un pequeño problemilla... Tengo unas 9000 variables que he contrastado con 1 en concreto con el test de wilcoxon. He calculado el p-valor, y queria corregirlo con el permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace esta corrección, pero te pide que le pongas las variables con las observaciones y te hace el test (según he entendido). Yo solo quiero

To All How does one get a list of functions from a loaded package so that one can then get the appropriate help for each of the functions. Currently my method is based on a lot of trial-and-error. Here's an example of what I mean... >From this forum I learn that an interesting package called "multtest" exists on Bioconductor. I then use R Console's "Packages" --

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

You can get help on the whole package by > help(package="multtest") which is likely pretty close to what you want. There's the index etc for the package on the web as well. You can also just look in the package's installation directory. If it's loaded you can do an ls(2) say if it loaded in position 2, to get all objects in the package. Reid -----Original Message-----

Hi, This is a very basic question, but I would like to undestand hist(). I thought that the hist( , freq=FALSE) should provide the relative frequencies (probabilities), and so they should sum 1, however: set.seed(2) ah <- hist(rnorm(100), freq=F) sum(ah$intensities) [1] 2 set.seed(2) bh <- hist(rlnorm(100), freq=F) sum(bh$intensities) [1] 0.4999996 I'm getting similar figures with

On Thu, Jan 13, 2000 at 17:34:10, Andre Lucas wrote: > Subject: /dev/urandom > On Thu, Jan 13, 2000 at 09:24:01AM -0700, SysProg - Nathan Paul Simons wrote: > > On Thu, 13 Jan 2000, Ben Taylor wrote: > > > > > On Thu, 13 Jan 2000, Max Shaposhnikov wrote: > > > > why ssh1.27 doesn't requre /dev/urandom on solaris? > > > > i think the

It's both in 2.6 and recent 2.6 (for RH ASS2.1 you'll probably need to copy the latest 2.4 defintion, but I don't care for obsolete junk). Index: src/super.c =================================================================== --- src/super.c (revision 1014) +++ src/super.c (working copy) @@ -799,7 +799,7 @@ /* get first two blocks */ for (i=0; i<2; i++) { - bhs[i] = getblk

Dear all, I'm working on a project that links to the BH package (http://cran.r-project.org/web/packages/BH/index.html). My packages doesn't call entry points which might terminate R nor write to stdout/stderr instead of to the console. However, it seems some of the codes in the BH package might. At any rate, when I include some boost headers such as boost/math/distributions/ through BH,

Hi I'm trying to compile the "bh" C program from the Olden benchmark to one bc file. # compile source files into an LLVM bitcode file llvm-gcc -emit-llvm -c args.c -o args.bc -w -DTORONTO llvm-gcc -emit-llvm -c newbh.c -o newbh.bc -w -DTORONTO llvm-gcc -emit-llvm -c util.c -o util.bc -w -DTORONTO llvm-gcc -emit-llvm -c walksub.c -o walksub.bc -w -DTORONTO # To link files together

checks IO error in ocfs2_get_sector(). this patch is based on 1.4 git. Signed-off-by: Wengang wang <wen.gang.wang at oracle.com> -- Index: fs/ocfs2/super.c =================================================================== --- fs/ocfs2/super.c (revision 128) +++ fs/ocfs2/super.c (working copy) @@ -1203,6 +1203,12 @@ static int ocfs2_get_sector(struct super unlock_buffer(*bh);

Hi, here is the second version of OCFS2 quota fixes with Joel's comments fixed. Also I've added a patch defining counts of credits for quota operations as Joel asked. Honza

always use the 2.6 variants and fix up for 2.4 under the hood Index: src/journal.c =================================================================== --- src/journal.c (revision 1156) +++ src/journal.c (working copy) @@ -105,9 +105,17 @@ return status; } -#else -#define ocfs_journal_start journal_start -#define ocfs_journal_stop journal_stop + +#define journal_start(journal, nblocks) \ +

The following series of patches attempts to detach metadata I/O from struct inode. They are currently tied together pretty tightly. Metadata reads happen via the ocfs2_read_blocks() functions, writes via both jbd2 and ocfs2_write_blocks(). - Each inode has a cache of associated metadata blocks stored on its ip_metadata_cache member. The ocfs2_read/write_blocks() functions take a struct

Folks, The projection pursuit regression function in the base R seems to crash when the optimization level is set to zero, i.e. the initial ridge terms are accepted without refitting. I encountered this problem in an out-of-sample prediction exercise using predict. But further investigation suggests the issue is with the ppr fit and predict just sppeds up the crash. The other optlevels seem to be

Dear List, I have been trying to use p.adjust() to do BH multiple test correction and have gotten some unexpected results. I thought that the equation for this was: pBH = p*n/i where p is the original p value, n is the number of tests and i is the rank of the p value. However when I try and recreate the corrected p from my most significant value it does not match up to the one computed by the

Hi, I did some more in-depth testing of OCFS2 quota code, especially with ECC feature enabled and spotted some problems. First four patches fix them. I need the fifth patch to be able to mount OCFS2 filesystem with 2.6.31-rc3. The sixth patch fixes a potential problem when quota syncing interval is updated while the cluster is running (which is not possible currently). Joel, could you please

The following 6 patches cleanup the jbd code and kill about 200 lines. First of 4 patches can apply to 2.6.13-git8 and 2.6.13-mm2. The rest of them can apply to 2.6.13-mm2. fs/jbd/checkpoint.c | 179 +++++++++++-------------------------------- fs/jbd/commit.c | 101 ++++++++++-------------- fs/jbd/journal.c | 11 +- fs/jbd/revoke.c | 158