[BioC] affy - read.celfile
Thu, 20 Jun 2002 21:37:11 +0200
On Thu, Jun 20, 2002 at 12:47:13PM -0700, David O. Nelson wrote:
> In the past (six months ago?), I noticed this type of problem too. What
> I found was that the read routines had gotten confused by differences in
> the encoding for newlines on PCs and Unix. In my case, the .cdf files
> were first transferred to a PC and then copied over to a Unix system. I
> first encountered this back when things were done by perl scripts, where
> the errant behavior was more explicit and could be easily debugged.
thanks for the pointer... but what puzzles me is that the Affymetrix
imaging software generating the CEL from the images only exists
(to my humble knowledge) for Windows...
...so technically all CEL files are coming from Windows...
...my wild guess would be that a local Perl hero messed up something in
the files... (and as advertised before in this very same list the parser
is designed to parse *Affymetrix* files rather than Affymetrix flavored
> However, I recently made the same mistake *again* with the C-based code,
> and the result was the symptoms you describe (Fool me once, shame on
> you; fool me twice, shame on me :-). Running it on a PC produced the
> expected results.
> In your case, was the .cdf file (or maybe the .cel file) read onto a PC
> and then transferred to Unix (or vice versa)?
> 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
...too bad... I missed a chance to reply that contributions to improve
things are also welcome...
> Dr. David O. Nelson
> Lawrence Livermore National Laboratory
> Box 808, L-441
> Livermore CA 94551
> On Thu, 2002-06-20 at 04:27, Wolfgang Huber wrote:
> > read.celfile (from package affy version 1.1.0) keeps hanging with cel files exported from dChip version 1.2. I am not sure how standards-conform the dChip-export is, but in any case it would seem useful for read.celfile to produce an intelligible error message rather than just hanging.
> > I managed to work around this by commenting the lines
> > ff@masks <- .Call("getIndexExtraFromCEL", ...
> > ff@outliers <- .Call("getIndexExtraFromCEL", ...
> > Wolfgang.
> > Dr. Wolfgang Huber
> > http://www.dkfz.de/abt0840/whuber
> > DKFZ
> > Dep. Molecular Genome Analysis
> > 69120 Heidelberg
> > Germany
> > _______________________________________________
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