search for: phenodata

...4-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: bioconductor-bounces at stat.math.ethz.ch on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo err...

...ow my subset function as it is subset.ExpressionSet <- function(x,subset=NULL,verbose=TRUE,...){ # subset is used to subset on rows # ... is used to make multiple conditions on columns based on pData # list of conditions is handled in ... stopifnot(is(x,"ExpressionSet")) phenoData <- pData(x) listCriteria <- list(...) if (is.null(subset)) subset <- rep(TRUE,nrow(exprs(x))) subset <- subset & !is.na(subset) retainedCriteria <- list() tmp <- sapply(names(listCriteria), function(critname) { if(!critname %in% colnames(phenoData)){...

...d) <- c("type","tumor","time","id"); pdN <- list(type = "Cellline/xenograft",tumor="primary,secondary,cellline",time = "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9") # Initialize exprSet object pD <- new("phenoData", pData=pd, varLabels=pdN); # This is my eSet!!! metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log), phenoData=pD) I get the following error: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead Can someone suggest me...

...e,quote = FALSE, sep = "\t", row.names = TRUE, > col.names = TRUE) > testFile [1] "C:\\DOCUME~1\\Jaswanth\\LOCALS~1\\Temp\\RtmpXrUE8T\\file2ea6bb3" > eSet <- read.exprSet(testFile) Warning messages: 1: read.exprSet is deprecated, use readExpresionSet instead 2: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 3: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 4: The exprSet class is deprecated, use ExpressionSet instead 5: The exprSet class is deprecated, use ExpressionSet instead 6: The exprSet class is deprec...

...residuals, weights *** caught segfault *** address 0xc609000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, normalize = normalize, background = background, bgversion = bgversion, destructive = destructive, cdfname = cdfname)...

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") bitmap(...

...-------- http://clarezoe.googlepages.com/1.png http://clarezoe.googlepages.com/2.png http://clarezoe.googlepages.com/3.png ------------- Errors also show in the terminal as below, ------------- > Error: no function to return from, jumping to top level In addition: Warning messages: 1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 2: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead Error in exprs(RawAffyData) : no function to return from, jumping to top level -------------- I'm running R version 2.6.1 under Linux Ubuntu 7.1...

..."colnames", "colnames<-", "description", "description<-", "exprs", "exprs<-", "length", "[", "[[", "[[<-", "pData", "phenoData", "phenoData<-", "show") System: R 2.1.0 on Suse9.2 Linux box -- Florian Hahne <f.hahne at dkfz-heidelberg.de>

..."colnames", "colnames<-", "description", "description<-", "exprs", "exprs<-", "length", "[", "[[", "[[<-", "pData", "phenoData", "phenoData<-", "show") System: R 2.1.0 on Suse9.2 Linux box -- Florian Hahne <f.hahne at dkfz-heidelberg.de>

...assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59 total) varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2 varMetadata: labelDescription channel phenoData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59 total) varLabels: sampleID tissue ... Annotation (5 total) varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.feinberg.hg18...

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below, > rna.data<-exprs(justRMA(f...

...allation. (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) > showMethods("[") Function "[": x = "ANY" x = "container" x = "phenoData" x = "exprSet" x = "aafList" x = "aafTable" > library(annaffy) (annaffy loads Biobase in .First.lib) > showMethods("[") Function "[": x = "ANY" x = "aafList" x = "aafTable"

..." "AD_Ctrl_5.CEL" [5] "AD_Ctrl_6.CEL" "AD_Traite_10.CEL" "AD_Traite_11.CEL" "AD_Traite_7.CEL" [9] "AD_Traite_8.CEL" "AD_Traite_9.CEL" > test <- read.celfiles(cel.files) Platform design info loaded. > phenoData(test) <- read.AnnotatedDataFrame("phenoData.txt", header = TRUE, row.name=1) > class(test) [1] "GeneFeatureSet" attr(,"package") [1] "oligoClasses" > class(phenoData) [1] "standardGeneric" attr(,"package") [1] "method...

..... ..@ other : list() > .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots > .. .. .. .. ..@ .Data:List of 1 > .. .. .. .. .. ..$ : int [1:3] 1 0 0 > ..@ assayData :<environment: 0x1078636e8> > ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots > .. .. ..@ varMetadata :'data.frame': 21 obs. of 1 variable: > .. .. .. ..$ labelDescription: chr [1:21] " Patient ID" " Date of diagnosis" " Gender of the...

Full_Name: Guy W. Tillinghast Version: 2.8.0 OS: Windows XP professional Submission from: (NULL) (24.248.24.3) I am encountering difficulty asking R to manipulate the correct columns in Expression Set class (object 4). I download the ALL data with: library(golubEsets) data(Golub_Merge) Note, the data has the samples not in order. This is not R's fault (at least not that I can tell): >

...ee 3h3 GSM286036.CEL three 6h1 GSM286037.CEL six 6h2 GSM286038.CEL six 6h3 GSM286039.CEL six library(affy) library(limma) library(vsn) pd <- read.AnnotatedDataFrame("er_for_affy.txt", header = TRUE, row.names = 2) pData(pd) #### load a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE) #### normalize x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.param = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method = "medianpolish") ### genes with highest variation library(hgu133plus2.db) rsd &...

...eywords: methods > > ### ** Examples > > library(yeastRNASeq) > data(geneLevelData) > data(yeastGC) > > sub <- intersect(rownames(geneLevelData), names(yeastGC)) > > mat <- as.matrix(geneLevelData[sub,]) > > data <- newSeqExpressionSet(mat, + phenoData=AnnotatedDataFrame( + data.frame(conditions=factor(c("mut", "mut", "wt", "wt")), + row.names=colnames(geneLevelData))), + featureData=AnnotatedDataFrame(data.frame(gc=yeastGC[sub]))) > >...

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...again: > data <- ReadAffy() > data AffyBatch (storageMode: lockedEnvironment) assayData: NA features, NA samples element names: exprs protocolData sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL (12 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL (12 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: drosophila2 when I start the analysis I get the following error message: &gt...

...;gilbellosta at gmail.com> Description: Package for the analysis of Taqman experiments License: TBA carlos at kropotkin:pcrAnalysis$ cat NAMESPACE import(methods, Biobase, outliers) exportPattern("^tqmn") exportClasses("pcrExprSet") exportMethods(task, "task<-", phenoData.sort) But now, the load of the packages fails. If I try to run carlos at kropotkin:tmp$ R CMD check pcrAnalysis I get the following log: * checking for working latex ... OK * using log directory '/tmp/pcrAnalysis.Rcheck' * using R version 2.4.1 (2006-12-18) * checking for file 'pcrA...