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"

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@fhcrc.org>
Date: Fri, 29 Jun 2007 16:23:15 -0500
To: "Cornell, John E" <cornell@uthscsa.edu>
Cc: Bioconductor <bioconductor@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@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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> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org



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