regenerate CEL file from analyzed data
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J. Greenbaum ▴ 20
@j-greenbaum-5391
Last seen 10.3 years ago
Hi all, I have an odd request.... I was wondering if there is a way to create a CEL file from processed data. We have a user here who needs to deposit their data in GEO for publication, but they have lost their original CEL file as the experiments were done 8 years ago. So, I was wondering if any of the Bioconductor modules (or any tool at all) might have the functionality to take a list of probe sets and intensity values and create a CEL file. I realize this is a long shot, but I thought I would throw it out there. Thanks in advance! -Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum@liai.org La Jolla Institute for Allergy and Immunology [[alternative HTML version deleted]]
probe probe • 832 views
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@benilton-carvalho-1375
Last seen 4.8 years ago
Brazil/Campinas/UNICAMP
Really depends on the definition of "processed data". If by that you mean that the user only has the results after something like RMA, there's nothing you can do to generate a CEL file from that. If the user has the intensity values prior to preprocessing (ie., probe-level data), then one suggestion is to use the affxparser package (createCel/updateCel). b On 11 July 2012 03:55, J. Greenbaum <jgbaum at="" liai.org=""> wrote: > Hi all, > > > I have an odd request.... > > > I was wondering if there is a way to create a CEL file from processed data. We have a user here who needs to deposit their data in GEO for publication, but they have lost their original CEL file as the experiments were done 8 years ago. So, I was wondering if any of the Bioconductor modules (or any tool at all) might have the functionality to take a list of probe sets and intensity values and create a CEL file. I realize this is a long shot, but I thought I would throw it out there. > > > Thanks in advance! > > > -Jason > > > > > > > -- Jason Greenbaum, Ph.D. > Manager, Bioinformatics Core | jgbaum at liai.org > La Jolla Institute for Allergy and Immunology > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks Benilton, All I have is a list of probeset names and the normalized intensity values...no probe level data. So what I would need to do is to generate the probe level data that would produce these normalized intensity values and then use createCel. Has anyone attempted this before? -J -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum@liai.org La Jolla Institute for Allergy and Immunology ----- Original Message ----- > From: "Benilton Carvalho" <beniltoncarvalho@gmail.com> > To: "J. Greenbaum" <jgbaum@liai.org> > Cc: bioconductor@r-project.org > Sent: Wednesday, July 11, 2012 3:14:37 AM > Subject: Re: [BioC] regenerate CEL file from analyzed data > Really depends on the definition of "processed data". If by that you > mean that the user only has the results after something like RMA, > there's nothing you can do to generate a CEL file from that. > If the user has the intensity values prior to preprocessing (ie., > probe-level data), then one suggestion is to use the affxparser > package (createCel/updateCel). > b > On 11 July 2012 03:55, J. Greenbaum <jgbaum@liai.org> wrote: > > Hi all, > > > > > > I have an odd request.... > > > > > > I was wondering if there is a way to create a CEL file from > > processed data. We have a user here who needs to deposit their > > data in GEO for publication, but they have lost their original CEL > > file as the experiments were done 8 years ago. So, I was wondering > > if any of the Bioconductor modules (or any tool at all) might have > > the functionality to take a list of probe sets and intensity > > values and create a CEL file. I realize this is a long shot, but I > > thought I would throw it out there. > > > > > > Thanks in advance! > > > > > > -Jason > > > > > > > > > > > > > > -- Jason Greenbaum, Ph.D. > > Manager, Bioinformatics Core | jgbaum@liai.org > > La Jolla Institute for Allergy and Immunology > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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You cannot do this. Kasper On Wed, Jul 11, 2012 at 12:16 PM, J. Greenbaum <jgbaum at="" liai.org=""> wrote: > Thanks Benilton, > > All I have is a list of probeset names and the normalized intensity values...no probe level data. So what I would need to do is to generate the probe level data that would produce these normalized intensity values and then use createCel. Has anyone attempted this before? > > -J > > -- Jason Greenbaum, Ph.D. > Manager, Bioinformatics Core | jgbaum at liai.org > La Jolla Institute for Allergy and Immunology > > ----- Original Message ----- > >> From: "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> >> To: "J. Greenbaum" <jgbaum at="" liai.org=""> >> Cc: bioconductor at r-project.org >> Sent: Wednesday, July 11, 2012 3:14:37 AM >> Subject: Re: [BioC] regenerate CEL file from analyzed data > >> Really depends on the definition of "processed data". If by that you >> mean that the user only has the results after something like RMA, >> there's nothing you can do to generate a CEL file from that. > >> If the user has the intensity values prior to preprocessing (ie., >> probe-level data), then one suggestion is to use the affxparser >> package (createCel/updateCel). > >> b > >> On 11 July 2012 03:55, J. Greenbaum <jgbaum at="" liai.org=""> wrote: >> > Hi all, >> > >> > >> > I have an odd request.... >> > >> > >> > I was wondering if there is a way to create a CEL file from >> > processed data. We have a user here who needs to deposit their >> > data in GEO for publication, but they have lost their original CEL >> > file as the experiments were done 8 years ago. So, I was wondering >> > if any of the Bioconductor modules (or any tool at all) might have >> > the functionality to take a list of probe sets and intensity >> > values and create a CEL file. I realize this is a long shot, but I >> > thought I would throw it out there. >> > >> > >> > Thanks in advance! >> > >> > >> > -Jason >> > >> > >> > >> > >> > >> > >> > -- Jason Greenbaum, Ph.D. >> > Manager, Bioinformatics Core | jgbaum at liai.org >> > La Jolla Institute for Allergy and Immunology >> > >> > >> > >> > >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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