.CEL file
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@prabhakar-ghorpade-6464
Last seen 9.6 years ago
Hi,    How can I view .CEL file? Is it possible to make dummy .CEL file for analysis? Regards, Prabhakar Dr. Ghorpade Prabhakar B. PhD Scholar ( Veterinary Biochemistry), IVRI, Izatnagar, Bareilly, U.P., India [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 12 hours ago
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Hi Prabhakar, On Thursday, March 27, 2014 4:32:27 PM, prabhakar ghorpade wrote: > Hi, > How can I view .CEL file? Is it possible to make dummy .CEL file for analysis? Can you expand on this a bit? What exactly are you trying to do? The celfile format is quite complicated, so creating a dummy file is likely to be more work than just getting some data from say, GEO or ArrayExpress and doing whatever you want. As for viewing a celfile, depending on what you mean by that, there are multiple options. 1.) If the celfile is text, you can just send it to stdout using 'cat'. Or if it is binary you can use the celfile converter to make it text, and then use cat (http://www.affymetrix.com/support/developer/downloads/Tools/CelFileCo nversion.ZIP) 2.) You could use the various functions in affxparser (readCel, readCelHeader, readCelIntensities, etc). 3.) You could use functions in affyio, either directly or via the affy package. Or if the array you care about is a more modern version, then you could use oligo and the respective pdInfoPackage. Or probably use some functions in xps that I don't know about. Best, Jim > > Regards, > Prabhakar > > Dr. Ghorpade Prabhakar B. > PhD Scholar ( Veterinary Biochemistry), > IVRI, > Izatnagar, > Bareilly, U.P., > India > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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@prabhakar-ghorpade-6464
Last seen 9.6 years ago
Did You tried BRB Array Tool. It uses Excel. Dr. Ghorpade Prabhakar B. PhD Scholar ( Veterinary Biochemistry), IVRI, Izatnagar, Bareilly, U.P., India On Friday, 28 March 2014 2:35 AM, James W. MacDonald <jmacdon@uw.edu> wrote: OK, well in that case good luck! I don't think I can help you with that, but maybe some of the functions I pointed out will be helpful. Best, Jim On 3/27/2014 4:59 PM, prabhakar ghorpade wrote: > Thanks for reply james, >            I want to create .CEL file which looks like file from > machine but with smaller data set. I am interested to see if I can > perform same analysis in excel as in R. > > > > regards, > prabhakar > /Dr. Ghorpade Prabhakar B./ > /PhD Scholar ( Veterinary Biochemistry),/ > /IVRI,/ > /Izatnagar,/ > /Bareilly, U.P.,/ > /India/ > > > On Friday, 28 March 2014 2:19 AM, James W. MacDonald <jmacdon@uw.edu> > wrote: > Hi Prabhakar, > > On Thursday, March 27, 2014 4:32:27 PM, prabhakar ghorpade wrote: > > Hi, > >    How can I view .CEL file? Is it possible to make dummy .CEL file > for analysis? > > Can you expand on this a bit? What exactly are you trying to do? > > The celfile format is quite complicated, so creating a dummy file is > likely to be more work than just getting some data from say, GEO or > ArrayExpress and doing whatever you want. > > As for viewing a celfile, depending on what you mean by that, there are > multiple options. > > 1.) If the celfile is text, you can just send it to stdout using 'cat'. > Or if it is binary you can use the celfile converter to make it text, > and then use cat > (http://www.affymetrix.com/support/developer/downloads/Tools/CelFile Conversion.ZIP) > > 2.) You could use the various functions in affxparser (readCel, > readCelHeader, readCelIntensities, etc). > > 3.) You could use functions in affyio, either directly or via the affy > package. Or if the array you care about is a more modern version, then > you could use oligo and the respective pdInfoPackage. Or probably use > some functions in xps that I don't know about. > > Best, > > Jim > > > > > > > Regards, > > Prabhakar > > > > Dr. Ghorpade Prabhakar B. > > PhD Scholar ( Veterinary Biochemistry), > > IVRI, > > Izatnagar, > > Bareilly, U.P., > > India > > >    [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]
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BRB array tools uses R and bioconductor tools to process the celfiles. The only thing it does in Excel is to make comparisons after the arrays have been processed. And as I said before, I can't help you with this. There are any number of ways to process raw Affymetrix data that are fast, free and already in existence. This is a solved problem, so if you want to solve it again using Excel, then have at it. But I wouldn't expect that many people want to spend much time helping you. Best, Jim On Thursday, March 27, 2014 5:39:32 PM, prabhakar ghorpade wrote: > Did You tried BRB Array Tool. It uses Excel. > > Dr. Ghorpade Prabhakar B. > PhD Scholar ( Veterinary Biochemistry), > IVRI, > Izatnagar, > Bareilly, U.P., > India > > > > On Friday, 28 March 2014 2:35 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > > OK, well in that case good luck! I don't think I can help you with that, > but maybe some of the functions I pointed out will be helpful. > > Best, > > Jim > > > On 3/27/2014 4:59 PM, prabhakar ghorpade wrote: >> Thanks for reply james, >> I want to create .CEL file which looks like file from >> machine but with smaller data set. I am interested to see if I can >> perform same analysis in excel as in R. >> >> >> >> regards, >> prabhakar >> /Dr. Ghorpade Prabhakar B./ >> /PhD Scholar ( Veterinary Biochemistry),/ >> /IVRI,/ >> /Izatnagar,/ >> /Bareilly, U.P.,/ >> /India/ >> >> >> On Friday, 28 March 2014 2:19 AM, James W. MacDonald <jmacdon at="" uw.edu=""> >> wrote: >> Hi Prabhakar, >> >> On Thursday, March 27, 2014 4:32:27 PM, prabhakar ghorpade wrote: >>> Hi, >>> How can I view .CEL file? Is it possible to make dummy .CEL file >> for analysis? >> >> Can you expand on this a bit? What exactly are you trying to do? >> >> The celfile format is quite complicated, so creating a dummy file is >> likely to be more work than just getting some data from say, GEO or >> ArrayExpress and doing whatever you want. >> >> As for viewing a celfile, depending on what you mean by that, there are >> multiple options. >> >> 1.) If the celfile is text, you can just send it to stdout using 'cat'. >> Or if it is binary you can use the celfile converter to make it text, >> and then use cat >> (http://www.affymetrix.com/support/developer/downloads/Tools/CelFil eConversion.ZIP) >> >> 2.) You could use the various functions in affxparser (readCel, >> readCelHeader, readCelIntensities, etc). >> >> 3.) You could use functions in affyio, either directly or via the affy >> package. Or if the array you care about is a more modern version, then >> you could use oligo and the respective pdInfoPackage. Or probably use >> some functions in xps that I don't know about. >> >> Best, >> >> Jim >> >> >> >>> >>> Regards, >>> Prabhakar >>> >>> Dr. Ghorpade Prabhakar B. >>> PhD Scholar ( Veterinary Biochemistry), >>> IVRI, >>> Izatnagar, >>> Bareilly, U.P., >>> India >> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 > >> >> >> > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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