similar to: Rhelp

Hello ... I've noticed that some of our Bioconductor 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 <-

Hello All, I need your help. I am analysing affymetrix data and have to select the probe-set that 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

A package uses VignetteEngine: knitr; the package itself does not Suggests: knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R CMD check fails indicating that a package required for checking is not declared. Is it really the intention that the original package duplicate Suggests: knitr? This is only with a recent R. In detail, with $ Rdev --version|head -3 R Under

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 session to reproduce the error: ...

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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

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

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Thanks to Dave and everyone who has contributed to ferret and acts_as_ferret! Man, can I not wait until I get this up and working on my project. Just the fuzzy search alone will be worth it. I''m having problems with rebuilding the index. My database includes Unicode entries, and I have configured the rest of Rails to correctly use it. On the initial index creation, I get this

There are certain queries that I can execute that will cause a completely repeatable segmentation fault at the point where the search or search_each leaves my control and goes into the ferret libraries. I tried deleting my indexes and recreating them, and even so the exact same queries seg fault repeatedly after. Usually a one character change will make them succeed. Changing away from a

Hello, I am trying to make a heatmap in R and am having some trouble. I am very new to the world of R, but have been told that what I am trying to do should be possible. I want to make a heat map that looks like a gene expression heatmap (see http://en.wikipedia.org/wiki/Heat_map). I have 43 samples and 900 genes (yes I know this will be a huge map). I also have copy numbers associated with

Dear R gurus, I have a very embarrassingly parallelizable job that I am trying to speed up with snow on our local cluster. Basically, I am doing ~50,000 t.test for a series of micro-array experiments, one gene at a time. Thus, I can easily spread the load across multiple processors and nodes. So, I have a master list object that tells me what rows to pick up for each genes to do the t.test from

Hi there, I am a bioinformatician working in DFCI. I am new to R. Yesterday I installed the R-1.7.1 to my Linux (since I am not able to find R-1.8 on the webpage). But I have some package installation problems ... 1. install.packages2() function isn't available. If I type at R prompt: >install.packages2("Biobase") Error: couldn't find function

Dear R list, I think my question maybe easy for you but I really spent entire day to resolve 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....

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

I testing Puppet 0.19.3. If we decide to use it, we''d deploy it across several thousand hosts. The method described for creating client certificates described in the documentation - running "puppetd --server <server> --waitforcert 60 --test" and "puppetca --sign <client>" - is not practical for our installation. I''ve tried creating

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

Hey all, I'm currently trying to build an R package and don't really know what to make of the error message I'm getting. I couldn't find anything helpful online so hopefully somebody here can give me a couple of pointers. I see the following when I try to build: s$ R CMD build --verbose r_package_files/ Warning: unknown option '--verbose' * checking for file

Hi, After updating R-2.12 on the Bioconductor build system about 1 week ago (we update R every 4-6 weeks for our devel builds), we've started to see something never seen before on Windows: for some BioC packages, 'R CMD build' would produce no output at all (0 byte) and, of course, no source tarball. Even though, the code returned by the command is 0! See an example of this is here:

Hello everyone, I have a data frame (tt), see below (I only show 2 genes, actually I have a lot): group gene1 gene2 Control 28.9776 9.9355 Control 28.9499 10.0997 Control 29.5468 14.2995 Control 29.5246 13.9561 Test1 29.1864 9.7718 Test1 29.2048 10.0388 Test1 34.9563 11.9509 Test1 34.9464 11.8909 Test2 36.9566 14.5316 Test2 37.1309 14.5188 Test2 36.1017