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kst ▴ 20
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Naomi Altman ★ 6.0k
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You are in luck. All you need to do is read the first few sections of the affy manual, and you will see that this is easily done in 4 or 5 lines of code. --Naomi Altman At 03:50 PM 4/16/2006, kst wrote: >hi, > I need to do summarizations of the probe intensity values for > each probeset of Affymetrix data in excel(.csv) format, by RMA, > GCRMA and MAS5. Can you please suggest me how to do it in R? or is > there any code available? > Thank-you for your help. > kavita > > >--------------------------------- > > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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Actually, if the data are .csv files then they most likely have already been processed using either MAS5 or GCOS. In that case you won't be able to do RMA or GCRMA. For that you need the .CEL files. However, as Naomi noted the first few sections of the affy vignette should help get you going if/when you get the celfiles. Best, Jim Naomi Altman wrote: > You are in luck. All you need to do is read the first few sections > of the affy manual, and you will see that this is easily done in 4 or > 5 lines of code. > > --Naomi Altman > > At 03:50 PM 4/16/2006, kst wrote: > >>hi, >> I need to do summarizations of the probe intensity values for >>each probeset of Affymetrix data in excel(.csv) format, by RMA, >>GCRMA and MAS5. Can you please suggest me how to do it in R? or is >>there any code available? >> Thank-you for your help. >> kavita >> >> >>--------------------------------- >> >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>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 > > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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I may have seen CEL files being saved as .xls, .csv, .txt as well. The easiest thing is to ask how many .csv files there are. If there are one .csv file per array, then can you post the first 30 lines or so. It might just be a case of renaming the files. Regards, Adai On Mon, 2006-04-17 at 08:58 -0400, James W. MacDonald wrote: > Actually, if the data are .csv files then they most likely have already > been processed using either MAS5 or GCOS. In that case you won't be able > to do RMA or GCRMA. For that you need the .CEL files. > > However, as Naomi noted the first few sections of the affy vignette > should help get you going if/when you get the celfiles. > > Best, > > Jim > > > > Naomi Altman wrote: > > You are in luck. All you need to do is read the first few sections > > of the affy manual, and you will see that this is easily done in 4 or > > 5 lines of code. > > > > --Naomi Altman > > > > At 03:50 PM 4/16/2006, kst wrote: > > > >>hi, > >> I need to do summarizations of the probe intensity values for > >>each probeset of Affymetrix data in excel(.csv) format, by RMA, > >>GCRMA and MAS5. Can you please suggest me how to do it in R? or is > >>there any code available? > >> Thank-you for your help. > >> kavita > >> > >> > >>--------------------------------- > >> > >> > >> [[alternative HTML version deleted]] > >> > >>_______________________________________________ > >>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 > > > > > > Naomi S. Altman 814-865-3791 (voice) > > Associate Professor > > Dept. of Statistics 814-863-7114 (fax) > > Penn State University 814-865-1348 (Statistics) > > University Park, PA 16802-2111 > > > > _______________________________________________ > > 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 > >
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