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getcolproc = function(files){
path = paste(files$path, "/", sep="")
procfile = files$processedArchive[1]
ph = try(read.AnnotatedDataFrame(basename(files$sdrf), path = path, row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, varMetadata.char = "$", quote="\""))
derivedMatrixCol = getSDRFcolumn("DerivedArrayMatrix",varLabels(ph))
derivedFileCol = getSDRFcolumn("DerivedArrayFile",varLabels(ph))
if(length(derivedMatrixCol) != 0)
skiplines = 1
else if(length(derivedFileCol) != 0)
skiplines = 0
else
warning("Unable to find Derived Data column in SDRF")
coln = scan(file.path(procfile),what = "",nlines = 1, skip = skiplines, sep = "\t")
return(unique(coln))
}
getcolraw = function(rawfiles){
rawfile = rawfiles[1]
coln = scan(file.path(rawfile),what = "",nlines = 1, sep = "\t")
return(coln)
}
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