search for: genefilt

...ioconductor code was running drastically slower under current R-devel vs. current R-patched - one example is below using a ttest. I have the following snippet of code that demonstrates the problem while avoiding "real" code that takes an extremely long time to finish on R-devel: library(genefilter) data(eset) eset$cov1 z <- ttest(eset$cov1, p=0.01) gf <- filterfun(z) system.time(genefilter(eset, gf)) (this requires the genefilter & Biobase packages from Bioconductor) Using R-1.7.0p I had the following output: > data(eset) > eset$cov1 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2...

...hat has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of 'genefilter' package but it's not well documented; and I do not know how to implement the 'findLargest' function. At this point I have: esetRMA <- rma(mydata) Could anybody guide me on how can I select single probeset with median expression from multiple probe-sets corresponding to single...

Hi, I discover that when I save a workspace containing a genefilter (pkg from Bioconductor) object I cannot open no more after. I have to restore the .RData file from a backup to be able to start R again. I didn't upgrade to Version 2.2 but I'm not sure that it will solve the problem. Did anyone have encounter the same problem? Below is a short r sessi...

...s is only with a recent R. In detail, with $ Rdev --version|head -3 R Under development (unstable) (2014-06-14 r65947) -- "Unsuffered Consequences" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) trying to check the Bioconductor genefilter package leads to $ Rdev --vanilla CMD check genefilter_1.47.5.tar.gz * using log directory ?/home/mtmorgan/b/Rpacks/genefilter.Rcheck? * using R Under development (unstable) (2014-06-13 r65941) * using platform: x86_64-unknown-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file...

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Hi, R-help group, I kinda meeting a question when using R-2.12.0(Previous version is 2.10.0): When I typed "library("Biobase")", everything is alright! But when I type "library("genefilter")", it doesn't work! And echo this: Error in library.dynam(lib, package, package.lib) : DLL 'RSQLite' not found: maybe not installed for this architecture? Error: package/namespace load failed for 'genefilter' Please someone tell me what's wrong...

Hello, I am trying to run R on my Mac (OS10.5.6) and am having trouble installing and running packages (genefilter in particular in Bioconductor) I've tried re-installing R and it hasn't solved the issue. Thanks, ~Nicole Slusher

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

...sion 2.6.7. Installing Bioconductor version 2.6 packages: [1] "affy" "affydata" "affyPLM" "affyQCReport" [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:...

...download.packages(pkgs, destdir = tmpd, available = available, **************************************************************** I did go to http://cran.us.r-project.org/src/contrib/PACKAGES to check the packages available there, there are quite few ... Many packages, such as Biobase, annotate and genefilter, are not included. Could you please give me some clue? I do appreciate! Sincerely, Rong

...esolve it. Say I have a matrix, rows are 6000 genes, columns(1-6) are 3 genotypes (a,b,c) with 2 repeat. I have to use two groups each time for t-test, a vs. c or b vs. c, but I dont know how to write correct codes. Below is my codes, the last two lines are needed to be corrected.... library("genefilter") ef <- exprs(esetsub) kk <- factor(esetsub$genotype == c("a", "c")) tt <- rowttests(ef[,c(1,2,5,6)], kk) ps. column 1-6 is a,a,b,b,c,c depending on the document, the kk should be a factor.. Any suggestions are really appreciated!! Best regards, Hui-Yi...

Dear list: I know this may be an old question. I know how to install the packages to a different directory, for example, /home/zrl/tmp and I know how to load it >library("genefilter",lib.loc="/home/zrl/tmp") but I found some package(for example package A) will have to load some other packages as well, and this time package A will look for the package in the original installation directory not the "/home/zrl/tmp". My question is, how could I tell R...

...2.2 of BioConductor. Will install the following packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" Anything that I install aft...

...tic': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes ----------------------------------- * installing *source* package 'pRRophetic' ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import by 'genefilter::Anova' when loading 'pRRophetic' ** help No man pages found in package 'pRRophetic' *** installing help indices ** building package indices Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 38 elements ERROR: installing packa...

.../bioc-LATEST/MotIV/liverpool-buildsrc.html (the content of this page is updated every day) Note the: RetCode: 0 PackageFile: None and the lack of output! This seems to happen randomly for a couple of packages every day. Today it's for MotIV only. Last time I checked, it was charm and genefilter. Before that, they were 2 other packages. Note that the only thing that changed on our Windows build machine liverpool (Windows Server 2003 R2 (32-bit)) is that R-2.12.0 was updated to 2010-06-11 r52254. Let me know if I can help in any way. Thanks, H. -- Herv? Pag?s Program in Computationa...

....5246 I'd like to calculate p values: Test1 vs Control and Test2 vs Control respectively for Gene1. Similar calculate performed for Gene2. I tried: sapply(levels(fac), function(x) t.test(tt1$gene1, tt$gene1[which(fac==x)])$p.value) # I don't really understand how it works, I copied from genefilter. where: fac=as.factor(tt$group) It seemed to work for first column. I don't know how to use apply() to make it work on rest of column because I used tt$gene1 specifically. Or whatever method that works Thank you in advance. Junyu [[alternative HTML version deleted]]

...GG 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 survival rat2302 "1.8.1" "1.11.5" "1.6.5" "1.11.13" "1.11.2" "2.7.9" "1.11.8" "2.28" "1.12.0" affy affyio Biobase "1.11.6" "1.1....

...I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only specified probesets within my eset file. Can anyone tell me how I would begin to approach this? I have looked into using the genefilter() function but can't figure out if it can take the right parameters (i.e. specific probe set id's). Thanks in advance, -M This is the code I used to generate my topTable > fit <- lmFit(eset, design) > cont.matrix <- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design) &...

..."1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12" "1.11.4" "1.13.6" &quo...

..."1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12" "1.11.4" "1.13.6" &quo...