[BioC] Generating .CHP files from .CEL files

Henrik Bengtsson hb at biostat.ucsf.edu
Mon Nov 1 21:30:37 CET 2010

CEL files contain the raw data.  That should be on GEO.  With CEL
files and a complete verbatim description/code of the analysis one can
ideally regenerate the results.

CHP files contain processed signals/summarized signals/parameter
estimates - not raw data.  CHP files are typically generated by
Affymetrix software tools only.  If your analysis was using, say,
Bioconductor tools, you never generated CHP files.  If so, it doesn't
make sense for GEO to ask for them.

My $.02


On Mon, Nov 1, 2010 at 1:23 PM, Janet L Smith <janet_s at mit.edu> wrote:
> Hi Everyone,
> I need to submit some affy chip data (Mouse 430 2) to GEO. This is an
> old project that I picked up from someone else, and I have the .CEL
> files, but no .CHP files.
> GEO seems to really want .CHP files. Is there a way to generate them
> from .CEL files? Or is there an alternative that someone can
> recommend?
> Thanks,
> Janet Smith
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