Question: intended behavior of plotPCA and AffyBatch objects?
0
gravatar for Jenny Drnevich
12.6 years ago by
Jenny Drnevich2.2k
Jenny Drnevich2.2k wrote:
Hi Jim, I just upgraded to R 2.5 and Bioconductor 2.0, and I noticed a change in the behavior of plotPCA. In R 2.4 and affycoretools 1.7.5, plotPCA could take an AffyBatch object, even though the help file does say it only supports exprSet, ExpressionSet and matrices (I just noticed!). I looked through the code, and in Bioconductor 1.9, if 'eset' is an AffyBatch object, a call to ' is(eset, "exprSet")' returned true, but in R 2.5 it returns false. The newest documentation for class AffyBatch still says it extends the exprSet class, which I know is (or will be) deprecated. I guess plotPCA was never intended to be called on an AffyBatch object, and I can get around it by using pm(eset) in the call, but I did want to point out the change with the AffyBatch class. I don't know if this was intended behavior or not, or if the AffyBatch class will be updated to extend the ExpressionSet class... which makes this more of a general affy question than affycoretools, I guess! Cheers, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
affy affycoretools • 616 views
ADD COMMENTlink modified 12.6 years ago by James W. MacDonald52k • written 12.6 years ago by Jenny Drnevich2.2k
Answer: intended behavior of plotPCA and AffyBatch objects?
0
gravatar for James W. MacDonald
12.6 years ago by
United States
James W. MacDonald52k wrote:
Hi Jenny, I never intended plotPCA() to be used with an AffyBatch, so the behavior is (now) as intended. Unless your AffyBatch contains normalized PM values, I am not sure how useful a PCA plot might be. But maybe I am missing something? Anyway, AffyBatch now extends the eSet class instead of exprSet, which as you mentioned is soon to be deprecated. Since an AffyBatch is not really an extension of an ExpressionSet (or an exprSet for that matter), extending eSet is a more logical choice. > extends("AffyBatch") [1] "AffyBatch" "exprSet" "annotatedDataset" "VersionedBiobase" "Versioned" > R.version.string [1] "R version 2.4.1 (2006-12-18)" > extends("AffyBatch") [1] "AffyBatch" "eSet" "VersionedBiobase" "Versioned" > R.version.string [1] "R version 2.5.0 (2007-04-23)" As you mentioned, you can always extract the PM probes and call plotPCA() on that. I'm not sure I want to change the behavior of plotPCA() to work with AffyBatches (or the eSet class in general), but I am always open to reasonable arguments. Best, Jim Jenny Drnevich wrote: > Hi Jim, > > I just upgraded to R 2.5 and Bioconductor 2.0, and I noticed a change > in the behavior of plotPCA. In R 2.4 and affycoretools 1.7.5, plotPCA > could take an AffyBatch object, even though the help file does say it > only supports exprSet, ExpressionSet and matrices (I just noticed!). > I looked through the code, and in Bioconductor 1.9, if 'eset' is an > AffyBatch object, a call to ' is(eset, "exprSet")' returned true, > but in R 2.5 it returns false. The newest documentation for class > AffyBatch still says it extends the exprSet class, which I know is > (or will be) deprecated. I guess plotPCA was never intended to be > called on an AffyBatch object, and I can get around it by using > pm(eset) in the call, but I did want to point out the change with the > AffyBatch class. I don't know if this was intended behavior or not, > or if the AffyBatch class will be updated to extend the ExpressionSet > class... which makes this more of a general affy question than > affycoretools, I guess! > > Cheers, > Jenny > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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.
ADD COMMENTlink written 12.6 years ago by James W. MacDonald52k
Hi Jim, I don't mind that plotPCA working with an AffyBatch object previously was an unintended behavior that now has been 'fixed'. At some point, someone needs to change the documentation for class AffyBatch because it still says it extends class exprSet (with a broken link) instead of class eSet. Cheers, Jenny At 12:30 PM 4/27/2007, James W. MacDonald wrote: >Hi Jenny, > >I never intended plotPCA() to be used with an AffyBatch, so the >behavior is (now) as intended. Unless your AffyBatch contains >normalized PM values, I am not sure how useful a PCA plot might be. >But maybe I am missing something? > >Anyway, AffyBatch now extends the eSet class instead of exprSet, >which as you mentioned is soon to be deprecated. Since an AffyBatch >is not really an extension of an ExpressionSet (or an exprSet for >that matter), extending eSet is a more logical choice. > > > extends("AffyBatch") >[1] "AffyBatch" "exprSet" "annotatedDataset" >"VersionedBiobase" "Versioned" > > R.version.string >[1] "R version 2.4.1 (2006-12-18)" > > > extends("AffyBatch") >[1] "AffyBatch" "eSet" "VersionedBiobase" "Versioned" > > R.version.string >[1] "R version 2.5.0 (2007-04-23)" > >As you mentioned, you can always extract the PM probes and call >plotPCA() on that. I'm not sure I want to change the behavior of >plotPCA() to work with AffyBatches (or the eSet class in general), >but I am always open to reasonable arguments. > >Best, > >Jim > > >Jenny Drnevich wrote: >>Hi Jim, >>I just upgraded to R 2.5 and Bioconductor 2.0, and I noticed a >>change in the behavior of plotPCA. In R 2.4 and affycoretools >>1.7.5, plotPCA could take an AffyBatch object, even though the help >>file does say it only supports exprSet, ExpressionSet and matrices >>(I just noticed!). I looked through the code, and in Bioconductor >>1.9, if 'eset' is an AffyBatch object, a call to ' is(eset, >>"exprSet")' returned true, but in R 2.5 it returns false. The >>newest documentation for class AffyBatch still says it extends the >>exprSet class, which I know is (or will be) deprecated. I guess >>plotPCA was never intended to be called on an AffyBatch object, and >>I can get around it by using pm(eset) in the call, but I did want >>to point out the change with the AffyBatch class. I don't know if >>this was intended behavior or not, or if the AffyBatch class will >>be updated to extend the ExpressionSet class... which makes this >>more of a general affy question than affycoretools, I guess! >>Cheers, >>Jenny >>Jenny Drnevich, Ph.D. >>Functional Genomics Bioinformatics Specialist >>W.M. Keck Center for Comparative and Functional Genomics >>Roy J. Carver Biotechnology Center >>University of Illinois, Urbana-Champaign >>330 ERML >>1201 W. Gregory Dr. >>Urbana, IL 61801 >>USA >>ph: 217-244-7355 >>fax: 217-265-5066 >>e-mail: drnevich at uiuc.edu >>_______________________________________________ >>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. Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
ADD REPLYlink written 12.6 years ago by Jenny Drnevich2.2k
Jenny Drnevich wrote: > Hi Jim, > > I don't mind that plotPCA working with an AffyBatch object previously > was an unintended behavior that now has been 'fixed'. At some point, > someone needs to change the documentation for class AffyBatch because it > still says it extends class exprSet (with a broken link) instead of > class eSet. Fixed in devel. Best, Jim > > Cheers, > Jenny -- 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.
ADD REPLYlink written 12.6 years ago by James W. MacDonald52k
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