Generating .CHP files from .CEL files

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Janet L Smith ▴ 40

@janet-l-smith-4332

Last seen 10.2 years ago

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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ADD COMMENT • link updated 14.1 years ago by Henrik Bengtsson ★ 2.4k • written 14.1 years ago by Janet L Smith ▴ 40

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Henrik Bengtsson ★ 2.4k

@henrik-bengtsson-4333

Last seen 6 months ago

United States

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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 14.1 years ago Henrik Bengtsson ★ 2.4k

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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@stat.math.ethz.ch [mailto:bioconductor- bounces@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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 14.1 years ago Ochsner, Scott A ▴ 60

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I completely agree with Scott on this, i've tried all the GEO methods & GEOArchive is by far the easiest Mark On 02/11/2010, at 7:37 AM, Ochsner, Scott A wrote: > 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 >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 14.1 years ago Mark Cowley ▴ 910

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Thanks all - GEOArchive is indeed much better than the GEO Submission page. No need for .CHP files anymore... good. - Janet ________________________________________ From: Mark Cowley [m.cowley@garvan.org.au] Sent: Monday, November 01, 2010 5:21 PM To: Ochsner, Scott A Cc: Janet L Smith; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Generating .CHP files from .CEL files I completely agree with Scott on this, i've tried all the GEO methods & GEOArchive is by far the easiest Mark On 02/11/2010, at 7:37 AM, Ochsner, Scott A wrote: > 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 >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 14.1 years ago Janet L Smith ▴ 40

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