[BioC] affy - read.celfile

David O. Nelson daven@llnl.gov
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
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



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
> Dep. Molecular Genome Analysis 
> 69120 Heidelberg 
> Germany
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