search for: affydata

...sages: 1: In safeSource() : Redefining ?biocinstall? 2: In safeSource() : Redefining ?biocinstallPkgGroups? 3: In safeSource() : Redefining ?biocinstallRepos? > biocLite() Using R version 2.11.1, biocinstall version 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&quo...

Dear all, I was trying to normalize a subset of affy data those transcribe are either P or M (called pm_filter). I am able to normalize pm_filter subset by using RMA method, however MAS5 is not working. For RMA method, I used the following commend: est<-rma(affydata, subset=pm_filter). Could any help me; how do I do this by using MAS5 method? Regards, Anup Som -- Dr. Anup Som, Ph.D. Institute for Biostatistics and Informatics in Medicine and Ageing Research University of Rostock, Medical Faculty Ernst-Heydemann-Str. 8, 18057 Rostock, Germany Tel: +49 381...

...g: 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 requires version 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" &quo...

...Vignettes contain introductory material. > > To view, simply type 'openVignette()' or start with 'help(Biobase)'. > > For details on reading vignettes, see the openVignette help page. > > >Loading required package: affyio >Loading required package: affydata >Loading required package: Biobase >Loading required package: gcrma >Loading required package: matchprobes >Loading required package: reposTools >Loading required package: simpleaffy >Loading required package: genefilter >Loading required package: survival >Loading required...

...R/library/affyPLM' ** Restoring previous '/usr/lib64/R/library/affyPLM' The downloaded packages are in /tmp/RtmpY18969/downloaded_packages Warning message: installation of package 'affyPLM' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", I get these error messages after I type these commands on R : source("http://www.bioconductor.org/biocLite.R") biocLite() when I search for blas , I get this : $ locate blas | grep so /usr/lib/libgslcblas.so.0 /usr/lib/libgslcblas.so.0....

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

...thods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads CEL files and returns a matrix of PM, MM, or both. This function is more memory efficient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes to the affydata vignette. The previously deprecated express function has been completely removed. Lastly, most normalization routines for AffyBatches can now be called with the parameter type which specifies wh...

...thods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads CEL files and returns a matrix of PM, MM, or both. This function is more memory efficient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes to the affydata vignette. The previously deprecated express function has been completely removed. Lastly, most normalization routines for AffyBatches can now be called with the parameter type which specifies wh...

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

...0/library': ada Performs boosting algorithms for a binary response affy Methods for Affymetrix Oligonucleotide Arrays affycomp Graphics Toolbox for Assessment of Affymetrix Expression Measures affydata Affymetrix Data for Demonstration Purpose affyio Tools for parsing Affymetrix data files affyPLM Methods for fitting probe-level models affyQCReport QC Report Generation for affyBatch objects ALL A data package annaffy...

...l.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affy' had non-zero exit status >> 5: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affydata' had non-zero exit status >> 6: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'Biostrings' had non-zero exit status >> 7: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> d...

...#39; version, and missing dependency annotations will be less likely to occur. == Dependencies == Move of code to RPM organization; it would be preferred to occur as early as possible, but is not a full blocker. These packages will need to be rebuilt: * COPASI * R-abind * R-acepack * R-affy * R-affydata * R-affyio * R-ALL * R-AnnotationDbi * R-ape * R-argon2 * R-ascii * R-askpass * R-assertthat * R-AUC * R-backports * R-base64enc * R-Bessel * R-BH * R-biglm * R-bindr * R-bindrcpp * R-Biobase * R-BiocGenerics * R-BiocParallel * R-biomaRt * R-Biostrings * R-bit * R-bit64 * R-bitops * R-blob * R-brew...

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