[BioC] Problem with tkWidgets with 2.5.0 on Mac OS Tiger

[Robert Gentleman]

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]]
>>
>> _______________________________________________
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> 
> --
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
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> 

-- 
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