search for: readaffy

....0 isn't auto-completing paths properly as it used to. E.g. suppose I have: > dir("CEL/choe") [1] "chipC-rep1.CEL" "chipC-rep2.CEL" "chipC-rep3.CEL" "chipS-rep1.CEL" [5] "chipS-rep2.CEL" "chipS-rep3.CEL" Now if I do: ReadAffy("CEL/choe/ch<tab> # => ReadAffy("CEL/choe/chip ReadAffy("CEL/choe/chipC<tab> # => ReadAffy("CEL/choe/chipC-rep ReadAffy("CEL/choe/chipC-rep1<tab> # Nothing happens. in 2.4.1 that final line auto-completes properly to: ReadAffy("CEL/choe/chipC-...

Hi there, I got a problem when trying to read in a .cel file using ReadAffy(). R codes: require(affy) ReadAffy(filenames="CH1.CEL") It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console...

When I try to load cel files (hgu133a) using the ReadAffy() in R 1.8.1 command I get an error message: > x<-ReadAffy() Error: cannot allocate vector of size 102973 Kb Does anybody know what does this error mean and how to overcome it? I have tried to load the same data with R 1.7.1 and it works. There is also no error when I use R 1.8.1 to load m...

Hello, Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array) Im useing this script: library(matchprobes) library(affy) library(AnnotationDbi) library(hgu133plus2probe) library(hgu133aprobe) library(hgu133a.db) u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch u133a1 = ReadAffy() # reading hgu133a cel file into affybatch u133a2 = ReadAffy() # reading hgu133a cel file into affybatch data<-combineAffyBatch(list(u133p2,u133a1,u133a2),c("hgu133plus2probe","hgu133aprobe","hgu133aprobe&...

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") > filenames<-as.character(filenames) > filename...

Hi, I am running R 2.0.1.1. on Windows. It is a Dell Dimension with a 3.2 Ghz Processor and 4Gb RAM. When using the ReadAffy() function to read in 97 arrays, I get the below error messages: Error: cannot allocate vector of size 393529 Reached total allocation of 1024Mb: see help(memory.size) When I use the comman "memory.limit(size=4000)" to increase the memory size to the maximum available, I got a "NUL...

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact information: Title: Heter URL: www.bioconductor.org A 1 word abstract is available...

...e CEL files from Affymetrix Mouse Array 430_2 and am trying to get the the individual PM intensities (11 per gene) for each sample. I would like to write out this into a tab delimited text file. Where am I stalling? This is what I've done: Change dir(to where CEL files are saved) Data <- ReadAffy() eset <- rma(Data) write.exprs(eset, file="mydata.txt") With this I am only able to get the average intensities per gene not the intensity per probe of each gene. Please help me out. Kanan

Sir, Kindlly Guide me how to get the R CELFILES. I have install R but I cannat asses the command: Data <- ReadAffy() and I got the error: Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : No cel filennames specified and no cel files in specified directory:C:/Documents and Settings/pawan.k/Desktop. Wit regds, Pawan ________________________________ This e-mail contains PRIVILEGE...

...ably sound silly to most of you. Here is the code I have problems with: readcelfiles <- function() { require(tcltk) tt <- tktoplevel() tkgrid(tklabel(tt,text="Choose a directory!")) OnOK <- function() { fileDir<-tclvalue(tkchooseDirectory()) data.raw <- ReadAffy(celfile.path=fileDir) #return(data.raw) } OK.but <- tkbutton(tt,text="OK",command=OnOK) tkgrid(OK.but) tkfocus(tt) } So after clicking on my "OK" button, I choose my directory and read the cel-files. But now I want to return the object to my workspace ... &qu...

Dear R-mailing list Hope you can help me. I am using R for windows to analyze my 107 HGU133Plus2.0 chips, however, R chrash when I try to use ReadAffy(). I want to buy a computer that can handle all these arrays, do you know how big a computer I need to buy? Best, Skov, Denmark [[alternative HTML version deleted]]

dear lady and gentalmen: i am gaoshan from kansas university. i used such coding to deal with gel data data <- ReadAffy() Warning messages: 1: In file(out, "wt") : cannot open file 'C:\Users\gaoshan\AppData\Local\Temp\RtmpvsyXOV\Rhttpd3f0b2e85': No such file or directory 2: In file(out, "wt") : cannot open file 'C:\Users\gaoshan\AppData\Local\Temp\RtmpvsyXOV\Rhttpd1d7427a' es...

...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 error with a capital N ($FileName) rather than lowercase n ($Filename) as in my target file..whoops. However this meant the filename argument was ignored without the error message(!) and instea...

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("clk-1.mva.jpg",width=15, height=12) mva.pairs(exprs(eset)[,c(19,20,21,22,23,24)],log.it=FALSE)...

Dear all, I am meeting some problems with memory allocation. I know it is an old issue, I'm sorry. I looked for a solution in the FAQs and manuals, mails, but without finding the working answer. I really hope you can help me. For instance, if I try to read micorarray data I get: > mab=ReadAffy(cdfname="hgu133plus2cdf") Error: cannot allocate vector of size 858.0 Mb > I get similar errors with smaller objects, smaller data sets or other procedures ("Error: cannot allocate vector of size 123.0 Mb"). I'm running R with Suse 11.1 Linux OS, on two Xeon processors...

Hi, when I try to import a microarray CEL batch, I get this error message: > myAB <- ReadAffy () Error in .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, : cannot allocate vector of length 1287151200 which, assuming the value is in bites, is below my RAM values (3 Gb recognized by Windows). The isse is, when I try to do memory.limit (size = 3000 ) the er...

...ll get the same error: Could not find array definition file ' hu6800cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I've tried specifying the cdfname file by using data<-ReadAffy(cdfname="hu6800cdf") but it still returns the same error. The version of R that I'm using is 2.15 and the bioconductor version is 2.10. Does anyone know how to solve this? Thanks, srod -- View this message in context: http://r.789695.n4.nabble.com/hu6800cdf-tp4630337.html Sent...

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of samples=6 number of genes=506944 annotation=ath1121501 notes= Warning messages: 1: Line starting '<TITLE>Error</TITLE> ...' is malformed! 2: Line starting '<BODY&g...

..."/") sampleFile <- paste(processedDir,"/",strInputAccession,"_RAWfilenames.txt",sep="") defaultExprs <- paste(processedDir,"/",strInputAccession,"_default_exprs.csv",sep="") if(file.exists(sampleFile)){ affyobj <- try(ReadAffy(filenames=read.table(sampleFile,as.is =T,header=FALSE)[,1])) if(class(affyobj)=="try-error"){ rm(affyobj) }else{ sampleNames(affyobj) <- sub("\\..*","",sampleNames(affyobj)) #get rid of .CEL etc extension, just keep GSM } } if(!exists("affyobj&q...

...the source files and installed in the directory /usr/lib64/R/library but when i try using those files, they show as not installed. Anybody encounter this problem before OR is there something else i am doing wrong? Following is the sequence of stpes i used first: 1) library(affy) 2) pcpc <- ReadAffy(sampleNames=c("107762","110662","110682","110792","110802","111301","111611","111781","111801","154272","160881")) 3) pc <- rma(pcpc) Error in library("hgu133plus2cdf", lib...