[BioC] affy - read.celfile
David O. Nelson
20 Jun 2002 12:47:13 -0700
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.
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
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
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", ...
> Dr. Wolfgang Huber
> Dep. Molecular Genome Analysis
> 69120 Heidelberg
> Bioconductor mailing list