similar to: memory issues with large data set

My machine has 4Gb of memory under WinXP Pro. Re-reading R for Windows FAQ 2.7 I discovered that I can use editbin to add the "/LARGEADDRESSAWARE" tag in the header without re-compiling, so that is what I did. I also check that it worked using dumpbin. I then edited my Boot.ini file to add the /3GB switch. Then I went to my R.0.0.1 patched that I modified as above and checked memory

Hi, R 2.5.0 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

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

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 formats Also, I tried

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

I have 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

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

Hi, I'm sort of a newbie to using R to deal with array data. I'm trying to create a simple filtering function, which outputs only the rows of a data frame that satisfies a specific criterion. I've set up an iterative loop to apply the condition to each row. I can create a new matrix and use rbind to fill it in row by row in the loop, before writing the whole matrix to file. But

Hello, I'm very new in working with tcl/tk in R and have a problem which will probably 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 <-

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

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="") >

Hello, My R skills are somewhere between novice and intermediary, and I am hoping that some of you very helpful forum members, whom I've seen work your magic on other peoples' problems/questions, can help me here. I have a matrix with the following format: (i) individual plants comprising many different genotype groups (i.e., a plant is genotype 1 or genotype 2 or genotype 3, etc). The

Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name ("FileName" instead of "Filename") which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers

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

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,

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

Hi, I'm using a command in bioconductor that seems to require a package called hu6800cdf. I've installed this properly but I still 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

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

Hey, I have code that can check the quality of a data set we're working with (expression data), and I'm having some trouble writing code that would make the expression data we have tie to other data we want to link it to (called phenotype data). Does anyone have any advice on how I could make a single object that would do this? Other relevant info: I want to use the pdata() function,