R/getcolproc.r

In ArrayExpress: Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

getcolproc = function(files){
    path = files$path
    procfile = files$processedFiles[1]
	ph = try(read.AnnotatedDataFrame(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))
	
	#TEMP############
	skiplines = 1
	#################
	
	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(path,procfile),what = "",nlines = 1, skip = skiplines, sep = "\t")
    return(unique(coln))
}

getcolraw = function(path, rawfiles){
    rawfile = rawfiles[1]
    coln = scan(file.path(path,rawfile),what = "",nlines = 1, sep = "\t")
    return(coln)
}