Question: ReadAffy widget fails for Annotated DataFrame
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gravatar for Kevin R. Coombes
11.8 years ago by
Kevin R. Coombes140 wrote:
Hi, Why does ReadAffy fail for the AnnotatedDateFrame part of an AffyBatch object? The session snapshot included below shows an error in using tkWidgets for AnnotatedDataFrames. I just upgraded to R 2.5.1 (so I would have the same version as the students in the microarray class I'm teaching), and code that worked in 2.4 fails to work in 2.5. Thanks for your help, Kevin > ReadAffy(widget=TRUE) Loading required package: tkWidgets Loading required package: widgetTools Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: DynDoc Error in read.AnnotatedDataFrame(sampleNames = sampleNames, widget = TRUE) : sorry, tkWidgets support not available for read.AnnotatedDataFrame > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tcltk" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: tkWidgets DynDoc widgetTools affy affyio Biobase "1.14.0" "1.14.0" "1.12.0" "1.14.2" "1.4.1" "1.14.1" >
ADD COMMENTlink modified 11.8 years ago by Martin Morgan ♦♦ 23k • written 11.8 years ago by Kevin R. Coombes140
Answer: ReadAffy widget fails for Annotated DataFrame
0
gravatar for Martin Morgan
11.8 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
Hi Kevin -- I guess the short answer is that, as the error message says, tkWidget support for AnnotatedDateFrame is not available! You'll have to revise your class notes to provide the required arguments to ReadAffy in a non-graphical way. Martin "Kevin R. Coombes" <krc at="" mdacc.tmc.edu=""> writes: > Hi, > > Why does ReadAffy fail for the AnnotatedDateFrame part of an AffyBatch > object? The session snapshot included below shows an error in using > tkWidgets for AnnotatedDataFrames. > > I just upgraded to R 2.5.1 (so I would have the same version as the > students in the microarray class I'm teaching), and code that worked in > 2.4 fails to work in 2.5. > > Thanks for your help, > Kevin > > > > ReadAffy(widget=TRUE) > Loading required package: tkWidgets > Loading required package: widgetTools > Loading required package: tcltk > Loading Tcl/Tk interface ... done > Loading required package: DynDoc > Error in read.AnnotatedDataFrame(sampleNames = sampleNames, widget = > TRUE) : > sorry, tkWidgets support not available for read.AnnotatedDataFrame > > sessionInfo() > R version 2.5.1 (2007-06-27) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "tcltk" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > tkWidgets DynDoc widgetTools affy affyio Biobase > "1.14.0" "1.14.0" "1.12.0" "1.14.2" "1.4.1" "1.14.1" > > > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org
ADD COMMENTlink written 11.8 years ago by Martin Morgan ♦♦ 23k
Sigh. Actually, when we last taught the course in Fall 2006, the version of R that students got in September was 2.3, since 2.4 came out in October. Having checked more carefully, the ReadAffy widget for phenoData or AnnotatedDataFrames (whichever was current) did *not* work in 2.4, but for a different reason. When the widget appeared and you pushed the button to "Read From File", you got the error message Error in new.env(hash = TRUE, parent = NULL) : use of NULL environment is defunct So, as far as I can tell, the last two "upgrades" of R/BioConductor have made the graphical interface in ReadAffy increasingly unusable. So, is there any chance that this will be made to work again some time in the (hopefully not too distant) future? Kevin Martin Morgan wrote: > Hi Kevin -- > > I guess the short answer is that, as the error message says, tkWidget > support for AnnotatedDateFrame is not available! You'll have to > revise your class notes to provide the required arguments to ReadAffy > in a non-graphical way. > > Martin > > "Kevin R. Coombes" <krc at="" mdacc.tmc.edu=""> writes: > >> Hi, >> >> Why does ReadAffy fail for the AnnotatedDateFrame part of an AffyBatch >> object? The session snapshot included below shows an error in using >> tkWidgets for AnnotatedDataFrames. >> >> I just upgraded to R 2.5.1 (so I would have the same version as the >> students in the microarray class I'm teaching), and code that worked in >> 2.4 fails to work in 2.5. >> >> Thanks for your help, >> Kevin >> >> >> > ReadAffy(widget=TRUE) >> Loading required package: tkWidgets >> Loading required package: widgetTools >> Loading required package: tcltk >> Loading Tcl/Tk interface ... done >> Loading required package: DynDoc >> Error in read.AnnotatedDataFrame(sampleNames = sampleNames, widget = >> TRUE) : >> sorry, tkWidgets support not available for read.AnnotatedDataFrame >> > sessionInfo() >> R version 2.5.1 (2007-06-27) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] "tcltk" "tools" "stats" "graphics" "grDevices" "utils" >> [7] "datasets" "methods" "base" >> >> other attached packages: >> tkWidgets DynDoc widgetTools affy affyio Biobase >> "1.14.0" "1.14.0" "1.12.0" "1.14.2" "1.4.1" "1.14.1" >> > >> >> _______________________________________________ >> 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 >
ADD REPLYlink written 11.8 years ago by Kevin R. Coombes140
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