[BioC] affy - read.celfile
Thu, 20 Jun 2002 23:03:15 +0200
thanks for your suggestion. As Laurent suggested, it's not the DOS/Unix
thing, but something else:
Indeed, the CEL files I was having trouble with were written from dChip on
a Windos machine, while I read them into R on a Unix machine.
And indeed, the CEL files do contain DOS-type newlines. However, that is
not the problem:
- I used other CEL files (e.g., http://www-genome.wi.mit.edu/mpr/lung/) that
also have DOS-newlines, and with whom read.celfile works fine.
- I did remove the extra ^M (LF) character, both with emacs and with
dos2unix; that did not help.
Taking a closer look at the problematic CEL files, they have no sections
headed [MASKS], [OUTLIERS]; while "normal" CEL files seem to have these
sections. So may I guess that the problem lies in here - read.celfile
expects these keywords in the CEL files, and when it doesn't find them,
it hangs. I guess that could be easily fixed.
> In the fine tradition of the R mailing list, I should now make a snide
> comment about you not giving us enough info, but I'll pass on that for
Right. I wasn't sure whether this would be an acceptable message to this
mailing list at all, since the troubling CEL files weren't written by
Affy software and one cannot expect the parser to cope with all sorts of
other stuff. So, my message came out in a sort of half-hearted manner...
Anyway, being rather unsophisticated with Affy and CEL files, I just
didn't know what more to supply, short of attaching the whole CEL file :)
Dr. Wolfgang Huber
Dep. Molecular Genome Analysis