justRMA => logarithmic data ?
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@heike-pospisil-1097
Last seen 10.2 years ago
Dear list members, I have an additional question concerning my affymetrix analysis. I performed justRMA on 79 CEL-files. data<-justRMA() The resulting expression data range from ~3 to ~14. min(exprs(data)) max(exprs(data)) Now, only for clarifying, are these values already logarithmised? I have read about the thresholds for the golub data that are much larger (100 and 16,000), but log2(16000)is ~14 - and so I think, that I have already logarithmic data. Am I right? Thanks a lot for your help. Best wishes, Heike -- Dr. Heike Pospisil Center for Bioinformatics, University of Hamburg Bundesstrasse 43, 20146 Hamburg, Germany phone: +49-40-42838-7303 fax: +49-40-42838-7312
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@arnemullersanofi-aventiscom-1086
Last seen 10.2 years ago
yes, the final output from RMA are log2 transformed. Arne > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Heike > Pospisil > Sent: 18 February 2005 09:29 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] justRMA => logarithmic data ? > > > Dear list members, > > I have an additional question concerning my affymetrix analysis. > > I performed justRMA on 79 CEL-files. > > data<-justRMA() > > The resulting expression data range from ~3 to ~14. > > min(exprs(data)) > max(exprs(data)) > > Now, only for clarifying, are these values already > logarithmised? I have read > about the thresholds for the golub data that are much larger > (100 and 16,000), > but log2(16000)is ~14 - and so I think, that I have already > logarithmic data. Am > I right? > > Thanks a lot for your help. > > Best wishes, > Heike > -- > Dr. Heike Pospisil > Center for Bioinformatics, University of Hamburg > Bundesstrasse 43, 20146 Hamburg, Germany > phone: +49-40-42838-7303 fax: +49-40-42838-7312 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Hello Arne, > yes, the final output from RMA are log2 transformed. thanks a lot for this reply. Best wishes, Heike > > Arne > > >>-----Original Message----- >>From: bioconductor-bounces@stat.math.ethz.ch >>[mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Heike >>Pospisil >>Sent: 18 February 2005 09:29 >>To: bioconductor@stat.math.ethz.ch >>Subject: [BioC] justRMA => logarithmic data ? >> >> >>Dear list members, >> >>I have an additional question concerning my affymetrix analysis. >> >>I performed justRMA on 79 CEL-files. >> >>data<-justRMA() >> >>The resulting expression data range from ~3 to ~14. >> >>min(exprs(data)) >>max(exprs(data)) >> >>Now, only for clarifying, are these values already >>logarithmised? I have read >>about the thresholds for the golub data that are much larger >>(100 and 16,000), >>but log2(16000)is ~14 - and so I think, that I have already >>logarithmic data. Am >>I right? >> >>Thanks a lot for your help. >> >>Best wishes, >>Heike >>-- >>Dr. Heike Pospisil >>Center for Bioinformatics, University of Hamburg >>Bundesstrasse 43, 20146 Hamburg, Germany >>phone: +49-40-42838-7303 fax: +49-40-42838-7312 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- Dr. Heike Pospisil Center for Bioinformatics, University of Hamburg Bundesstrasse 43, 20146 Hamburg, Germany phone: +49-40-42838-7303 fax: +49-40-42838-7312
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