search for: affyplm

hi all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o median_logPM.o medianPM.o medianpolish.o nthLargestPM.o PLM_modelmatrix.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o rlm...

...zeichnisse ... Erzeuge DESCRIPTION ... Erzeuge NAMESPACE ... Erzeuge Read-and-delete-me ... Kopiere Code-Dateien ... Erzeuge Hilfedateien ... Fertig. one of the classes in the package is a S3 packge and has the name "preprocess". using the package require various packages. one of them is affyPLM, which also have a S3 class named preprocess. Each time I'm using the program i get the message: > library(affyPLM) Lade nötiges Paket: affy Lade nötiges Paket: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bio...

...#39;m running the latest R on a presumably up to date Linux server. 'Doing something silly I'm sure, but can't see why my saved PLMset objects come out all wrong. To use an example: Setting up an example PLMset (I have the same problem no matter what example I use) > library(affyPLM) > data(Dilution) # affybatch object > Dilution = updateObject(Dilution) > options(width=36) > expr <- fitPLM(Dilution) This works, and I'm able to get the probeset coefficients with coefs(expr). until I save and try reloading: > save(expr, file="expr.RData&qu...

...ce() : 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" "limma"...

...ing RMA. When I tried to import the all the normalized expression data as a single text file and make a boxplot, it showed discrepancy among the sample groups. I tried to scale them or re-normalize them again, so that it can be used for further analysis. Unfortunately, I did not manage it on using AffyPLM package. Would you please help me out with this problem. Thanks in advance. Best regards, H. Nawaz -- View this message in context: http://r.789695.n4.nabble.com/scaling-on-normlized-data-set-tp2996771p2996771.html Sent from the R help mailing list archive at Nabble.com.

Dear Sirs, I am using both the Bioconductor adds on (Affy, AffyPLM,...) and the 'standard' R-package. I am trying to select a list of genes which all have expression values below a certain threshold. I have done this by creating a vector which has 0s where the expression is greater than the threshold and 1s where it is less than or equal to it. Multiplyin...

...ioconductor.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" "marray" &qu...

...ontain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from 'package:stats': resid, residuals, weights *** caught segfault *** address 0xc609000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, normalize, background, bgv...

...osoft '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 themselves, or adding more options under 'Vignettes'. Specific combinations of any 3 of: affycoretools, RWinEdt, affyPLM or affylmGUI can cause the crash. So far, I haven't been able to get it to crash without affycoretools, even if I load all the dependencies by themselves, but that may just be because I don't know of another package that adds to the menu bar. After playing around with this for a while,...

...(prada) -- Agilent arrays handling in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, B...

Hi everyone, I am having installation problems, but this is how it all started: I had some errors running the bioconductor package affyPLM that uses LAPACK/Blas > Pset <- fitPLM(Data) Background correcting PM Normalizing PM Fitting models /usr/local/lib/R/bin/exec/R: relocation error: /usr/local/lib/R/lib/libRlapack.so: undefined symbol: s_copy # thrown out of R .... I was using R version 2.4.0, so I decided to upgrade t...

...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 Annotation tools for Affymetrix biological metadata annotate Annotation for...

...ges(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'simpleaffy' had non-zero exit status >> 11: In install.packages(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...

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