similar to: Help with Affymetrix data

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

Dear all I apologize for cross-posting, but first it is accepted custom to thank the repliers and give a summary, and second I have still the feeling that this problem might be a general statistical problem and not necessarily related to microarrays only, but I might be wrong. First, I want to thank Robert Gentleman, Mark Kimpel and Mark Reiners for their kind replies. Robert Gentleman kindly

Hi, I am trying to read in my Affymetrix CEL files (48 files, total ~600 MB) but I keep getting memory errors. Can somebody please help me with this. Or is therea remote server I can send my data to for computation? Any help is much appreciated. Thanks Dr. Tristan Coram Postdoctoral Research Associate Research Plant Pathologist/Geneticist United States Department of

mogene10stprobeset.db is generated with AnnotationDbi for mouse gene array. I don't find a package that seems generated by AnnotationDbi for exon arrays on the webpage you mentioned. Is it correct? On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > Hi Peng, > > I am not completely clear from your post what you want. ?But most of our > annotation

I am looking for an online (easily accessible) form of the samples of genetic data for those with cancer and those without cancer. Can anyone direct me in the right place? Thanks, Jim [[alternative HTML version deleted]]

I don't know if this is the correct forum to ask the following question; however, when I search the aroma.affymetrix discussion group, it suggested that I should posted the question to r-help. Here it goes. I followed the instructions on aroma.affymetrix trying to install the packages; following are the steps: > install.packages(c("R.oo", "R.utils"),

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@biostatsun1

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

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

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 moe430 cel files. Thanks very much for any

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!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="") >

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

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

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 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,