UCSC links in the regions.xls file pointing to wrong genome build?

[Sebastian Burgstaller]

Hello everyone,

I am quite new to aroma.affymetrix, but so far, I was successfully using it and i really like it.

I did my first 190 SNP6 CNV arrays with the annotation files for hg19, using CB segmentation. But the UCSC links in the .xls file generated by CBS and in the regions.xls file generated by Chromosome Explorer point to hg18.

Did i miss to adjust some important settings, or could this be a minor bug?

Thank you for your answers!

[Marcin Krzystanek]

I think you need to have up to date files listed here:

http://aroma-project.org/chipTypes/GenomeWideSNP_6

... including the up to date cdf file

Best,

Marcin

--
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[Cristian Bassi]

Me too! I have this problem.....and all files are up to date! i don't
know....

On 7 Mag, 15:38, Marcin Krzystanek <kke...@gmail.com> wrote:
> I think you need to have up to date files listed here:http://aroma-project.org/chipTypes/GenomeWideSNP_6
>
> ... including the up to date cdf file
>
> Best,
>
> Marcin
>
> On Mon, May 7, 2012 at 1:34 PM, Sebastian Burgstaller <
>
>
>
>
>
>
>
> sebastian.burgstal...@gmail.com> wrote:
> > Hello everyone,
>
> > I am quite new to aroma.affymetrix, but so far, I was successfully using
> > it and i really like it.
>
> > I did my first 190 SNP6 CNV arrays with the annotation files for hg19,
> > using CB segmentation. But the UCSC links in the .xls file generated by CBS
> > and in the regions.xls file generated by Chromosome Explorer point to hg18.
>
> > Did i miss to adjust some important settings, or could this be a minor bug?
>
> > Thank you for your answers!
>
> > --
> > 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.
>
> > You received this message because you are subscribed to the Google Groups

> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.

[Henrik Bengtsson]

Hi,

everything is fine; you've got the correct annotation data files. The
only issue is that code writing that 'url' column added to the
regions.xls file is rather stupid, i.e. the genome version is hard
coded.

You can rewrite the regions.xls file with the correct UCSC Genome
Browser by passing argument 'hgVersion' (defaults to "hg18"):

process(ce, hgVersion="hg19")

To recreate the regions.xls file afterward, do:

writeRegions(ce, hgVersion="hg19")

or just do a search/replace in an editor.

DETAILS:
The defaults are current hardwired to getRegions() for the
CopyNumberSegmentationModel class, i.e.

> args(getRegions.CopyNumberSegmentationModel)
function (this, ..., url = "ucsc", organism = "Human", hgVersion = "hg18",
margin = 0.1, flat = FALSE, verbose = FALSE)

This is really old code/style. Ideally, the organism and the genome
version should be picked up from the annotation data. Second best, is
to have it specified when setting up the ChromosomeExplorer, e.g.

ce <- ChromosomeExplorer(..., hgVersion="hg19")

I'll add this to the todo list.

Sorry for the confusion.

/Henrik

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