Generating common variance from tumour/normal pair ratios

[Sathish Periyasamy]

I have completed the doCRMAv2 for tumour/ Normal pairs and obtained
the results in ChromosomeExplorer. However, I would like to find the
common variance (i.e. gains and loss, LOH) across these pairs.

I would be pleased if you could assist me to reach this milestone.

I am planning to take the following rout. Correct me if I am wrong.

pathname <- writeRegions(cns, verbose=verbose);
library("R.filesets");
db <- TabularTextFile(pathname);


regards,

Sathish

[Henrik Bengtsson]

Hi.

On Sat, May 5, 2012 at 1:12 PM, Sathish Periyasamy
<sathish.p...@gmail.com> wrote:
> I have completed the  doCRMAv2 for tumour/ Normal pairs and obtained
> the results in ChromosomeExplorer. However, I would like to find the
> common variance (i.e. gains and loss, LOH) across these pairs.
>
> I would be pleased if you could assist me to reach this milestone.
>
> I am planning to take the following rout. Correct me if I am wrong.
>
> pathname <- writeRegions(cns, verbose=verbose);

Method for doing such across sample summaries/analysis are not
provided by the aroma framework. But, given the tab-delimited text
file segmentation results written to file by writeRegions(), you may
be able to pass those results on to methods such as RAE
[http://www.ncbi.nlm.nih.gov/pubmed/18784837] and GISTIC
[http://goo.gl/eX1bX].

/Henrik

> library("R.filesets");
> db <- TabularTextFile(pathname);
>
>
> regards,
>
> Sathish
>

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