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Messages - Maaman

1
XCMS / "object 'xset' not found"
I've recently started using XCMS and R. I'm working on a rather large dataset (~40 files each 1gb) so I've made a "for loop" to split the computing into chunks:

for (i in 1:ceiling(length(datafiles)/blkSize))
  {ind <- ((i - 1) * blkSize + 1):min((i * blkSize),nfiles); xset[] <- xcmsSet(datafiles[ind],phenoData = design2[ind,,drop = FALSE])}; xset <- do.call(c,xSet)

when I execute this it runs the xcmsSet command for the first 4 files (for blkSize=4) and then gives the error message:

Error in xset[] <- xcmsSet(datafiles[ind], phenoData = design2[ind,  :
  object 'xset' not found

I've tried pre-creating an object named xset, the only type I got it to accept was an empty list, but that meant it loaded the entire list to memory negating the point of the loop.

Am i going at this the wrong way? I've seen others use similar loops and they don't appear to have the same problem.
Any help is appreciated.