[BioC] affy - read.celfile

Wolfgang Huber w.huber@dkfz-heidelberg.de
Thu, 20 Jun 2002 23:03:15 +0200

Hi David,

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
> now.

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 :)

Best regards

Dr. Wolfgang Huber
Dep. Molecular Genome Analysis 
69120 Heidelberg