[BioC] Generating .CHP files from .CEL files

[Ochsner, Scott A]

Janet,

Use the GEOArchive option to deposit Affy data to GEO.  Download the Excel template from GEO and fill in data as required.  You can easily upload your own processed values for your experiment.  

Scott  


Scott A. Ochsner, PhD
One Baylor Plaza BCM130, Houston, TX 77030
Voice: (713) 798-6227  Fax: (713) 790-1275 
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Henrik Bengtsson
Sent: Monday, November 01, 2010 3:31 PM
To: Janet L Smith
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Generating .CHP files from .CEL files

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

Henrik

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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