[BioC] Agilent - importing and reading problems

[Bernal-Mizrachi, Leon]

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) <- colnames(log.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/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

>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

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