search for: affyqcreport

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 AFFX-r2-Ec-bio...

...iocinstall? 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" "limma" [17] "marray"...

...t; "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. Does anyone have any suggestions? Thanks, A ______________________________________________________...

...e >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 package: splines >Welcome to 'affyQCReport' V 1.6-1 >Further information available at: www.bifix.org > mailto: craig.parman at bifix.org >Loading required package: ade4 >Loading required package: scatterplot3d > > > source("http://bioconductor.org/biocLite.R") > > biocLite("affycoretool...

...p 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 Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface a...

...ckages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affyPLM' had non-zero exit status >> 12: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affyQCReport' had non-zero exit status >> >> sessionInfo() >>> >> R version 2.8.0 (2008-10-20) >> i486-pc-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8...

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