[BioC] ReadAffy widget fails for Annotated DataFrame

[Kevin R. Coombes]

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"
>>  >
>>
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>