search for: multtest

...w 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" -- "Install package(s) from Bioconductor" to download "multtest". I then load "multtest" into my session using "Packages -- Load package..." I now want to investigate what functio...

Hello! I downloaded a package "multtest" (from bioconductor.org) in R, and installed it by 'R CMD <package>' (after unzipping and taring). The problem is when I say 'library(multtest)' in R, the following error is generated: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shar...

I have been running R CMD check for the first time on of our own packages, which otherwise builds, installs and runs just fine. The package depends on package akima and suggests package multtest; suggesting multtest is indicated because a) it loads a lot of other Bioconductor packages, very slowly, and b) it is only needed for one specific subroutine, which executes require(multtest) every time it's called. Now, when I run R CMD check on our package, it terminates when check...

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> >...

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 -...

...e: Ken Kompass Version: 2.2.0 OS: winXP pro (2002 version, SP2) Submission from: (NULL) (128.252.149.244) Using R2.2.0 I get this error msg when loading certain bioconductor libraries (depending on whether the library contains file named "all.rda" in R folder of library) : > library(multtest) Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file 'C:/PROGRA~1/R/R-22~1.0/library/multtest/R/all.rda' Error in library(multtest) : .First.lib failed for 'multtest' > The error occurs with loading...

Hi, Installing from binaries on Windows: > install.packages("multtest") Warning: dependency 'Biobase' is not available trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip' Content type 'application/zip' length 1645590 bytes (1.6 Mb) opened URL downloaded 1.6 Mb package 'multtest' succe...

Hi, With recent versions of R-devel, "R CMD check" complains about some "Rd files with unknown sections". hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz ... ... * checking Rd files ... WARNING Rd files with unknown sections: /home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd: notes /home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/MTP.Rd: notes See chapter 'Writing R documentation files' in manua...

Hi, thanks for the report - but it should have gone to the Bioconductor list, and the package maintainer, thanks. New versions of multtest and a few other packages will percolate up in the next few days to resolve the problem. Best wishes, Robert kompass at vision.wustl.edu wrote: > Full_Name: Ken Kompass > Version: 2.2.0 > OS: winXP pro (2002 version, SP2) > Submission from: (NULL) (128.252.149.244) > > &...

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

> 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

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

.... After installing the latest R2.4.0 on my computer, to my surprise the results are totally different from that calculated using R2.1.1. Even the example code doesn't work the same way under these two versions of R. Does anybody know what is going on? Thanks for any suggestions. library(multtest) data(golub) # golub.cl contains the class labels. golub.cl # Perform a SAM analysis for the two class unpaired case assuming # unequal variances. sam.out<-sam(golub,golub.cl,B=100,rand=123) sam.out # Obtain the Delta plots for the default set of Deltas plot(sam.out) Best Wei Zh...

...[5] "annaffy" "annotate" "Biobase" "biomaRt" [9] "Biostrings" "DynDoc" "gcrma" "genefilter" [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma" [17] "marray" "multtest" "vsn" "xtable" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11' Error in if (ok) { : missing value where TRUE/FALSE needed > biocLite() Using R version 2....

> 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 all_differ[[1]][, "BY...

Dear all, I am running R 2.4.1. > library(siggenes); > library(multtest); > cl<-rep(c(0,1),c(3,3)); > sub<-exprs(AffyExpData[,c(1:3,7:9)]); > gn<-geneNames(AffyRAwData); > sam.out<-sam(sub,cl,rand=123,gene.names=gn); We're doing 20 complete permutations > sam.out SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances...

I've been using SAS PROC MULTTEST to perform multiple comparisons on data that are not normally distributed by using the stepdown bootstrap procedures of Westfall and Young (1993). According to the SAS manual, "the bootstrap method creates pseudo-data sets by sampling observations with replacement from each within-stratum poo...

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 using my model parameters...

..."annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" Anything that I install after this gives me the same error. I tried uninstalling R 2.7.0 and installing R 2.6.2, and performing the same commands, as above, but the same thing happens....

...uot; "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [9] "base" other attached packages: Rgraphviz geneplotter XML GOstats Category hgu95av2 KEGG multtest xtable "1.11.9" "1.11.8" "0.99-8" "1.6.0" "1.4.1" "1.12.0" "1.8.1" "1.11.2" "1.3-2" RBGL annotate GO graph Ruuid limma genefilter...