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Hi John, John Cornell wrote: > Thank you Martin: > > The problem with tkWidgits also occurs with the Windows version. > > I am encountering problems with other Affy tools, as well. For example, when > I attempted to demonstrate the MAplot with data I had already analyzed, I > got the following error message. > >> MAplot(baboon.raw,col=densCols(exprs(baboon.raw)),cex=.6,cex.main=.7) > > Error in assayData(object) : no slot of name "assayData" for this object of > class "AffyBatch" I am sorry that you are having problems with some of the software, but it would help a lot if you could please provide the output of sessionInfo and if at all possible reproducible examples of failures, or at least some indication of the work flow that gets you to the problem you have reported here. In particular can you let us know where/how the baboon.raw data were created? And possibly what class they are? > > At this point, we are rolling back to 2.4 on all systems until these and > other unknown bugs are fixed in 2.5 and BioC 2.0 Well, that is unfortunately unlikely to happen without folks using the system and reporting bugs so that they can be addressed. We realize that this is sometimes frustrating from a users perspective and can only assure you that when reported, in sufficient detail, we do act on but reports quite quickly. > > Cheers, > > John E. Cornell, Ph.D. > Professor > Department of Medicine > Department of Epidemiology and Biostatistics > University of Texas Health Science Center, San Antonio > 7703 Floyd Curl Drive > San Antonio, Texas 78229-3900 > > ---------------- > > "Expectation, hope, intention towards possibility ... this is not only a > basic feature of human consciousness, but ... a basic determination within > reality as a whole." > > -- Ernst Bloch > -- The Principle of Hope, vol. 1 > > > > > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Date: Fri, 29 Jun 2007 16:23:15 -0500 > To: "Cornell, John E" <cornell at="" uthscsa.edu=""> > Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Conversation: [BioC] Problem with tkWidgets with 2.5.0 on Mac OS Tiger > Subject: Re: [BioC] Problem with tkWidgets with 2.5.0 on Mac OS Tiger > > Unfortunately, this means that tkWidgets cannot be used to > ReadAffy. This is a limitation of affy / Biobase, and not an issue > with your OS. You'll have to provide the information through the > command line. > > Martin > > John Cornell <cornell at="" uthscsa.edu=""> writes: > >> Hi Folks: >> >> I upgraded to R 2.5.0 for Mac OS X 10.4. I am using the widget=T option in >> ReadAffy( ) to read in a set of CEL files. The process starts fine but >> terminates when I click finish in the first frame. The following error >> message is printed. >> >> >> Error in read.AnnotatedDataFrame(sampleNames = sampleNames, widget = TRUE) : >> sorry, tkWidgets support not available for read.AnnotatedDataFrame >> >> Anyone know how to solve this problem. >> >> Cheers, >> >> John E. Cornell, Ph.D. >> Professor >> Department of Medicine >> Department of Epidemiology and Biostatistics >> University of Texas Health Science Center, San Antonio >> 7703 Floyd Curl Drive >> San Antonio, Texas 78229-3900 >> >> ---------------- >> >> "Expectation, hope, intention towards possibility ... this is not only a >> basic feature of human consciousness, but ... a basic determination within >> reality as a whole." >> >> -- Ernst Bloch >> -- The Principle of Hope, vol. 1 >> >> >> >> [[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 > > -- > Martin Morgan > Bioconductor / Computational Biology > http://bioconductor.org > > > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

John -- John Cornell <cornell at="" uthscsa.edu=""> writes: > Thank you Martin: > The problem with tkWidgits also occurs with the Windows version. ? Yes, the widget code is complicated to debug and hence difficult to transform to work with the AnnotatedDataFrame object that replaces phenoData. As I think I mentioned, this code is not specific to operating system. This has come up several times, how is the widget used -- reading files from disk? entering phenoData interactively? editing data frames to be transformed to phenoData? If one of these uses predominated, and especially if that use was 'reading files from disk', then this might make it more feasible to update tkWidgets. > I am encountering problems with other Affy tools, as well. For example, when I > attempted to demonstrate the MAplot with data I had already analyzed, I got > the following error message. >> MAplot(baboon.raw,col=densCols(exprs(baboon.raw)),cex=.6,cex.main=.7) > Error in assayData(object) : no slot of name "assayData" for this object of > class "AffyBatch" This is a version mis-match or, if baboon.raw has been serialized (saved to disk), an object that needs to have > baboon.fresh = updateObject(baboon.raw) to transform it to the current version. It is still possible and perhaps even likely that packages are expecting to work with the old-style AffyBatch, but many work with the new style. > At this point, we are rolling back to 2.4 on all systems until these > and other unknown bugs are fixed in 2.5 and BioC 2.0 > Cheers, > John E. Cornell, Ph.D. > Professor > Department of Medicine > Department of Epidemiology and Biostatistics > University of Texas Health Science Center, San Antonio > 7703 Floyd Curl Drive > San Antonio, Texas 78229-3900 > ---------------- > "Expectation, hope, intention towards possibility ... this is not only a basic > feature of human consciousness, but ... a basic determination within reality > as a whole." > -- Ernst Bloch > -- The Principle of Hope, vol. 1 > > ------------------------------------------------------------------ -------- > > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Date: Fri, 29 Jun 2007 16:23:15 -0500 > To: "Cornell, John E" <cornell at="" uthscsa.edu=""> > Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Conversation: [BioC] Problem with tkWidgets with 2.5.0 on Mac OS Tiger > Subject: Re: [BioC] Problem with tkWidgets with 2.5.0 on Mac OS Tiger > Unfortunately, this means that tkWidgets cannot be used to > ReadAffy. This is a limitation of affy / Biobase, and not an issue > with your OS. ?You'll have to provide the information through the > command line. > Martin > John Cornell <cornell at="" uthscsa.edu=""> writes: >> Hi Folks: >> >> I upgraded to R 2.5.0 for Mac OS X 10.4. I am using the widget=T option in >> ReadAffy( ) to read in a set of CEL files. The process starts fine but >> terminates when I click finish in the first frame. The following error >> message is printed. >> >> >> Error in read.AnnotatedDataFrame(sampleNames = sampleNames, widget = TRUE) : >> ????sorry, tkWidgets support not available for read.AnnotatedDataFrame >> >> Anyone know how to solve this problem. >> >> Cheers, >> >> John E. Cornell, Ph.D. >> Professor >> Department of Medicine >> Department of Epidemiology and Biostatistics >> University of Texas Health Science Center, San Antonio >> 7703 Floyd Curl Drive >> San Antonio, Texas 78229-3900 >> >> ---------------- >> >> "Expectation, hope, intention towards possibility ... this is not only a >> basic feature of human consciousness, but ... a basic determination within >> reality as a whole." >> >> -- Ernst Bloch >> -- The Principle of Hope, vol. 1 >> >> >> >> ??????[[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 > -- > Martin Morgan > Bioconductor / Computational Biology > http://bioconductor.org > -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org