[BioC] Problem with tkWidgets

[James W. MacDonald]

Hi Ignacio,

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 
biocLite().

Best,

Jim
>
>   -- output of sessionInfo():
>
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     tcltk     stats     graphics  grDevices utils    datasets
> [8] methods   base
>
> other attached packages:
> [1] tkWidgets_1.30.0   DynDoc_1.30.0      widgetTools_1.30.0 affy_1.30.0
> [5] Biobase_2.12.2
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.20.0         annotate_1.30.1       AnnotationDbi_1.14.1
>   [4] DBI_0.2-5             genefilter_1.34.0     limma_3.8.3
>   [7] marray_1.30.0         preprocessCore_1.14.0 RSQLite_0.10.0
> [10] splines_2.13.1        survival_2.36-10      xtable_1.5-6
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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