search for: simpleaffi

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD

Dear Madam/ Sir, I am using?R version 3.4.2.?I want to analyse microarray data. when I want to install "simpleaffy" package I get this error "package ?simpleaffy? is not available (for R version 3.4.2)". I have the same problem with?R version 3.3.2. Could you please help me to solve it? I am working with RStudio 0.99.903.exe. I also have problem in getting the new release of

Hello, After running R CMD check on my package I received the following error on package dependencies: * using log directory 'C:/z-zBackup/Nuvera Bio on Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck' * using R version 2.9.1 (2009-06-26) * using session charset: ISO8859-1 * checking for file 'nvNormalize/DESCRIPTION' ... OK * checking extension type ... Package *

Hi, I'm using a command in bioconductor that seems to require a package called hu6800cdf. I've installed this properly but I still get the same error: Could not find array definition file ' hu6800cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I've tried specifying

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

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Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

I am trying to use package ROCR to analyze classification accuracy, unfortunately there are some problems right at the beginning. Question 1) When I try to run demo I am getting the following error message > library(ROCR) > demo(ROCR) > if(dev.cur() <= 1) .... [TRUNCATED] Error in get(getOption("device")) : wrong first argument When I issue the command > dev.cur() it

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is