similar to: Help with multtest (rawp2adjp)

> 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

Dear everyone, I am trying to do a Wilcoxon one-sided test on my gene expression data. These are the data i have in R: data.matrix (matrix, numeric) containing all gene expression data (42 rows=genes, 42 columns=tumors), no column header or row names data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0 or class 1 for each column in data.matrix I want to do a

Hi- Is anyone working on multiple comparisons of means or post-hoc tests (ie: Tukey, Bonferroni) for R? I saw in the winter 98' archives of the R mailing lists that these tests had not been implemented yet, I was just wondering if I could look foward to having them. ;-) I also looked through the contributed packages and didn't see anything that offered such tests. I guess I could check

Hi All I would like to compute the raw p-value from permutation tests and I found mt.sample.rawp() from the package multtest almost similar to what I want to do. But in the function definition: mt.sample.rawp(V,classlabel,test="t",side="abs",fixed.seed.sampling="y",B=10000,na=.mt.naNUM,nonpara="n") I would like to choose my own t-test which is designed

Hello, I am relatively new to using R. I am using R version 2.8.0. I have a program that downloads stock data from Yahoo! Finance and stores it to a text file on my hard drive. The text file contains the date, opening price, high price, low price, closing price, volume and adjusted price (i.e., adjusted for dividends and splits). I want to read and manipulate the data in R. However, when I

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

Matt, Here's a Bonferroni-corrected multiple one-sample t-test that I wrote some years ago. It took a while to get it into R, as na.omit doesn't seem to handle vectors and I had to write a quick kludge (na.remove). Another more general point was that I discovered that the help page for t.test gives the name "parameters" for the degrees of freedom, as in S. However, the name

Hello all, I am calculating probabilities of association for terms in the GeneOntology database. I have ~4e7 probabilities and I would like to correct for multiple testing. At the moment I have something like the following: pv is a vector containing my 4e7 probabilities. To run the multiple testing corrections I do: mt <- mt.rawp2adjp(pv, proc="BH") Because of the size of

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" --

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

> From: Thomas Lumley [mailto:tlumley at u.washington.edu] > > Please don't send these messages to r-announce. r-announce is for > announcements. Isn't r-announce supposed to be moderated? I posted to r-announce about a minor update in randomForest and was rejected. I was told that it's meant for new or significant upgrades in packages, etc. Andy

Hi Nguyen, > Subject: [R] install "multtest" and "preprocessCore" packages in > Bioconductor library > Date: Wed, 30 Nov 2011 09:57:36 -0800 > From: UyenThao Nguyen <unguyen at tethysbio.com> > To: r-help <r-help at r-project.org> > CC: uth.nguyen at ucdavis.edu <uth.nguyen at ucdavis.edu> > > Hi All, > > I've tried to

Dear R community I sent a message out a while ago asking for help with multiple comparison tests for ANOVA's, but haven't had any response yet. I'm sending a final desperate plea. If I can't get this done in R I'm going to have to redo a whole lot of stuff in a commercial package, which I'm REALLY not keen to do! My problem is how to implement these tests in R. Below

Dear R-devel, I am trying to do something similar to dynamic length lists in R, but at C level. In R, that would be rather trivial: - determine the length of the list - create the list object - store the values for each component - access value components by using "[[" At C level, for a single component where I need to store a vector of length 5, I do: int *p_result; SEXP my_list =

Add a new constant ETH_P_802_3_MIN, the minimum ethernet type for an 802.3 frame. Frames with a lower value in the ethernet type field are Ethernet II. Also update all the users of this value that David Miller and I could find to use the new constant. Also correct a bug in util.c. The comparison with ETH_P_802_3_MIN should be >= not >. As suggested by Jesse Gross. Compile tested only.

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 everyone, i followed colins example and it worked perfectly but now i get this error ActionController::DoubleRenderError in UserController#login Render and/or redirect were called multiple times in this action. Please note that you may only call render OR redirect, and at most once per action. Also note that neither redirect nor render terminate execution of the action, so if you want to

Hi ! I've been trying to improve NV50 shader generation a bit the last couple of weeks, so here is what I've produced. I don't know if it's usable for you or just a pile of horrible hacks, but at least it makes some mesa demos render more correcly, p.e. the teapot (aside from mip-mapping issues of the floor texture), arbfplight, and I think the gears also didn't appear as they

Make use of tgsi_shader_info to determine how many nv50_regs we need to allocate, if program uses KIL, or writes DEPR. --- src/gallium/drivers/nv50/nv50_program.c | 284 ++++++++++++++----------------- 1 files changed, 129 insertions(+), 155 deletions(-) diff --git a/src/gallium/drivers/nv50/nv50_program.c b/src/gallium/drivers/nv50/nv50_program.c index e2adeca..c8157f1 100644 ---