Hi,
I finally got around to have a serious take at this and you're correct it
does no longer retrieve cytoband information from the GLAD package.
Instead it looks for a cytoband data file:
annotationData/genomes/<genome>/<genome>,cytobands(,<tag>)*.txt
In the aroma.core package, it will always find
annotationData/genomes/Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt
under system.file(package="aroma.core"). [I just added that hg17 tags
based on your information]. You should be able to update that to
hg19. Please consider contributing your annotation file to
aroma.core.
However, a bug was introduced causing aroma to fail locating this
file. Update to aroma.core v2.4.2 and it should work:
source("http://www.braju.com/R/hbLite.R";);
hbLite("aroma.affymetrix");
You can also verify that it works by:
sm <- CbsModel(...);
plot(sm, arrays=1, chromosomes=17);
/Henrik
PS. Kai, what is your last name and affiliation so I can credit you in
the NEWS file?
On Fri, Jan 13, 2012 at 8:42 AM, Kai <[email protected]> wrote:
> Thanks, Henrik. Does ChromosomeExplorer still look for the cytoband file in
> the GLAD package? I thought the latest version does not rely on GLAD
> anymore, rather it won't display a cytoband if it cannot find the
> information from within the aroma packages. Am I mistaken?
>
> Thanks,
> Kai
>
> --
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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