[BioC] Source code comments / read_abatch

[Ben Bolstad]

It is doing the right thing. Or at least what I think is the right
thing, since I (hazardly) wrote/designed that code. What it is
attempting to do is pass down a string identifying the CDF file used to
generate the CEL files (not the one you associate it with as an
AffyBatch for work in BioC), so that each and every file read agrees (ie
you are not trying to mix and match CEL files that should not be grouped
together).

Ben




> 
> 
> Particularly, I was wondering about this chunk of code in read.affybatch:
> 
> headdetails <- .Call("ReadHeader", as.character(filenames[[1]]),
> PACKAGE = "affyio")
> dim.intensity <- headdetails[[2]]
> ref.cdfName <- headdetails[[1]]
> if (is.null(cdfname)) cdfname <- ref.cdfName
> # ...
> exprs <- .Call("read_abatch", filenames, rm.mask, rm.outliers,
> rm.extra, ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio") ##
> HERE #1
> colnames(exprs) <- samplenames
> if (!sd) {
>   return(new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData
> = phenoData, nrow = dim.intensity[1], ncol = dim.intensity[2],
> annotation = cleancdfname(cdfname, addcdf = FALSE), description =
> description, notes = notes)) ## HERE #2
> }
> else {
> # ...
> }
> 
> 
> Shouldn't the line marked HERE #1 be using cdfname, NOT ref.cdfName?
> The line marked HERE #2 uses cdfname as it (I think) should.
> 
> I'm guessing this is just me not understanding the code (usually the case).
> 
> Your help is greatly appreciated.
> 
> 
> Cheers,
> John Woods
> 
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