search for: gcrma

Hi ! I would like to understand where do affinity.spline.coefs used in function compute.affinities come from ? library(gcrma) data(affinity.spline.coefs) affinity.spline.coefs X1 X2 X3 X4 X5 X1 -0.55004171 -0.58579091 -0.08870557 -0.47774242 0.23205570 0.58002746 X2 X3 X4 X5 X1 X2 0.61274425 0.10294309 0....

I run R 1.9.0 on windows 2000, and have the following libraries installed: affydata_1.3.1 affy_1.4.23 Biobase_1.4.10 DynDoc_1.3.14 gcrma_1.0.6 hgu133acdf_1.4.3 hgu95av2cdf_1.4.3 hgu95av2probe_1.0 matchprobes_1.0.7 moe430acdf_1.4.3 multcomp_0.4-6 mvtnorm_0.6-6 rae230acdf_1.4.3 reposTools_1.3.29 rgu34acdf_1.4.3 tkWidgets_1.5.1 widgetTools_1.2.7 1. The rma function (in affy library) always crashes. 2. When executing the sample code in...

I am receiving the following errors when trying to install gcrma and a number of other Bioconductor packages when the installWithVers flag is set to be TRUE. >source("http://www.bioconductor.org/getBioC.R"); >getBioC("gcrma", installWithVers=T); Running biocinstall version 2.0.7 with R version 2.5.0 Your version of R requires version...

Hello, I am using the following code to plot an MVA plot. library(affy) library(Biobase) library(limma) library(gcrma) pd<-read.phenoData("Clk.targets.2.txt",header=TRUE, row.names=1,as.is=TRUE,sep="\t") Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) Print(Data) eset <- gcrma(Data) write.exprs(eset, file="clk.6-23-05.txt")...

...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" "vsn" "xtable" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument '...

...Error in lm.fit(design, t(M)) : incompatible dimensions I will really appreciate if someone can help me understand this error message and possibly help me debug the problem. Thanks manisha Reference section xen1data<-ReadAffy() # Read Affy dataset cell files xen1dataeset<-gcrma(xen1data) # Normalize with GCRMA write.exprs(xen1dataeset,file="xen1_exprs") # write normalzed expression values >str(exprs(xen1dataeset)) num [1:22690, 1:2] 12.0 11.3 13.0 11.6 10.3 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:22690] "1415670_at"...

...ion 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] "multtest" "ROC" "vsn" "xtable" "affyQCReport"...

...oading required package: methods Welcome to Bioconductor Vignettes contain 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&...

...s" [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" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20"...

...s" [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" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20"...

...'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 package: splines >Welcome to 'affyQCReport' V 1.6-1 >Further...

...Lade nötiges Paket: affy Lade nötiges Paket: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Lade nötiges Paket: gcrma Lade nötiges Paket: preprocessCore Attache Paket: 'affyPLM' The following object(s) are masked from package:affyAnalysis : preprocess The following object(s) are masked from package:stats : resid, residuals, weights The preprocess command in the affyPLM...

...s" [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" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20"...

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...eTS) -- Packages for lab assay analysis and management (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 (arrayMagi...

...document tools e1071 Misc Functions of the Department of Statistics (e1071), TU Wien edd expression density diagnostics foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... gcrma Background Adjustment Using Sequence Information genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Grapics related functions for Bioconductor globaltest T...

...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" "0.8-0" XML GOstats Category genefilter survival "1.4-0" "2.0.4" "2.0....

...ll.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'vsn' had non-zero exit status >> 9: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'gcrma' had non-zero exit status >> 10: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'simpleaffy' had non-zero exit status >> 11: In install.packages(pkgs = pkgs, repos = repos, dependencies = >>...

...a management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not includ...

...a management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not includ...