Hello everybody, I am Leon Bernal-Mizrachi, I am and MD at Emory University. I'm a newbie in R and BioC, so please forgive me if my question is easy... I have done some expression experiments using Whole Human Genome Oligonucleotide Microarray in 4X44K format (cy3/cy5Cy). I am facing difficulties importing and reading my data to work in R. I have tried to follow the vignette from limma but I have been unsuccessful. This is what I have done: >setwd("C:/Users/Leon Bernal/Desktop/agilent leon data/AGILENT/TEXT_formatted_raw_data_files")pattern="US23502303") >files <- dir(desc.lines <- 9 >for ( ii in 1:length(files)) { tmp <- read.table( files[ii], sep="\t", as.is=T,header=T, skip = desc.lines, row.names=NULL, quote="", comment.char="") if ( ii == 1 ) { if ( !("gMeanSignal" %in% names(tmp) & "gBGMeanSignal" %in% names(tmp) & "Row" %in% names(tmp)) ) stop( "First data file",files.msp1[1]," is missing one of gMeanSignal, gBGMeanSignal, or 'Row' columns") ProbeName <- tmp$ProbeName ; GeneName <- tmp$GeneName X<-tmp$Col; Y<-tmp$Row log.intensity <- log.bg <- matrix( nr= dim(tmp)[1], nc=length(files)) colnames(log.intensity) <- colnameslog.bg) <- sub( ".txt","",files) real.genes <- union( grep("ref", tmp$accessions), union( grep("gb", tmp$accessions), grep("ens", tmp$accessions))) real.probes <- grep( "A_[0-9]",ProbeName) neg.controls <- grep("NegativeControl", tmp$GeneName ) # random probes are controls if ( length( neg.controls) == 0 ) stop("Unable to identify control probes") } if ( dim(tmp)[1] != dim( log.intensity)[1] ) { warning(files[ii]," has a different number of rows than ",files.pairs[1]); next } log.intensity[,ii] <- log2(tmp$gMeanSignal ) log.bg [,ii] <- log2(tmp$gBGMeanSignal) cat(ii,"..") } >controls<- setdiff(1:dim(tmp)[1], real.probes) >rm(tmp) >X.controls <- X[ controls ] >Y.controls <- Y[ controls ] >X <- X[ real.probes ] >Y <- Y[ real.probes ] >FeatureName <- GeneName[ controls ] >gene.names <- GeneName[ real.probes] >targets<-readTargets(Targets.txt) >library(limma) >targets<-readTargets("Targets.txt") >targets >RG<-read.maimages(targets$filename,source="agilent",path="C:/Users/Le on Bernal/Desktop/agilent leon data/AGILENT/TEXT_formatted_raw_data_files") Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file >RG<-read.maimages(files,source="agilent",path="C:/Users/Leon Bernal/Desktop/agilent leon data/AGILENT/TEXT_formatted_raw_data_files") Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file Does anybody has face similar problems?, and if so do you have any suggestion or path to guide me to solve this problems? Thanks Leon Leon Bernal-Mizrachi,MD Assistant Professor Hematology/Oncology Winship Cancer Institute Emory University Tel:(404) 778-1839 Fax: (404) 778-5520 This e-mail message (including any attachments) is for t...{{dropped:11}}