search for: annaffy

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: > library(Biobase) > library(annaffy) > showMeth...

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (128.102.184.81) annaffy 1.0.1 (in BioC CVS) fails to load. annaffy 1.0 (on the BioC web site) has the same problem. It looks like the load is failing because of a bug in completeSubclasses() in r-devel. It calls setIs() and doesn't specify an environment via the "where" argument. setIs() "where" d...

Dear all, I am currently analyzing a set of arrays hybe on the lattest affy Drosophila 2.0 GeneChip. I am trying to run simple annaffy analysis but can¹t find what is the name of the annotation file I need to use. Here is the output of the AffyBatch object I am using: > expData AffyBatch object size of arrays=732x732 features (16749 kb) cdf=Drosophila_2 (18952 affyids) number of samples=4 number of genes=18952 annotation=droso...

...) : 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" "multtest" &qu...

...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" "marray" "matchprobes" [16...

...=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" [7] "tools" "methods" "base" other attached packages: multtest rat2302cdf affycoretools annaffy xtable "1.13.1" "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0&qu...

...=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" [7] "tools" "methods" "base" other attached packages: multtest rat2302cdf affycoretools annaffy xtable "1.13.1" "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0&qu...

...s '/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.0.0.0 /usr/lib64/libblas.so.3.0 /usr/lib64/l...

...Depends. The version dependence will in a future release cause an update of XML when rtracklayer is installed, if needed (and available). (B) Things like (package stam) Depends: R (>= 2.7.0), GO.db (>= 2.1.3), Biobase (>= 1.99.5), pamr (>= 1.37.0), cluster (>= 1.11.10), annaffy (>= 1.11.5), methods (>= 2.7.0), utils (>= 2.7.0) are redundant: the versions of method and utils are always the same as that of R. And there is no point in having a package in both Depends: and Imports:, as Biostrings has. (C) There is no check on the version of a package s...

...=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" [7] "tools" "methods" "base" other attached packages: multtest rat2302cdf affycoretools annaffy xtable "1.13.1" "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0&qu...

...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 arules Mining Association Rules and Frequent Itemsets base The R B...

...ages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: made4 scatterplot3d ade4 affycoretools annaffy "1.8.0" "0.3-24" "1.4-2" "1.7.5" "1.6.1" xtable gcrma matchprobes biomaRt RCurl "1.4-3" "2.6.0" "1.6.0" "1.8.1" &quo...

...er or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes and ROC curves divided by overall expression. Also, all functions that work for hgu95a spike in now also work for hgu133a spike in experiment --- annaffy: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. --- Biobase: The generic func...

...er or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes and ROC curves divided by overall expression. Also, all functions that work for hgu95a spike in now also work for hgu133a spike in experiment --- annaffy: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. --- Biobase: The generic func...

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