[BioC] Problem with tkWidgets
James W. MacDonald
jmacdon at med.umich.edu
Mon Oct 3 15:09:42 CEST 2011
On 10/3/2011 6:46 AM, Ignacio López de Ullibarri [guest] wrote:
> I have found a problem with the tkWidgets package. When executing readAffy(widget=TRUE), the CEL files are visible on the left panel of the widget, but no the compressed ones (i.e. those with names *.CEL.gz). This contradicts Figure 1 of the \'affy\' vignette of the affy package.
> Is this actually a bug in the package? or could this be caused by some problem on my platform (Ubuntu 10.04)?
Yes, that is a bug. Surprisingly enough this bug has existed for years
now without being detected. Although these days there isn't a profit in
gzipping a celfile (you don't gain anything by gzipping a binary file),
so maybe that explains it.
Anyway, fixed in the devel version (1.31.6). This should propagate
through the build system and be available in 24 hours or so. Note that
you will need to use the devel version of R in order to get it via
> -- output of sessionInfo():
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-linux-gnu (64-bit)
>  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>  LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
>  LC_PAPER=en_GB.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  tools tcltk stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  tkWidgets_1.30.0 DynDoc_1.30.0 widgetTools_1.30.0 affy_1.30.0
>  Biobase_2.12.2
> loaded via a namespace (and not attached):
>  affyio_1.20.0 annotate_1.30.1 AnnotationDbi_1.14.1
>  DBI_0.2-5 genefilter_1.34.0 limma_3.8.3
>  marray_1.30.0 preprocessCore_1.14.0 RSQLite_0.10.0
>  splines_2.13.1 survival_2.36-10 xtable_1.5-6
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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