Hi.
On Mon, Apr 30, 2012 at 5:31 AM, Marcin wrote:
> Dear Henrik,
>
> I have a dataset in which my collaborators took two types of cancer
> cell lines and made a few single copy clones of them per cell line.
> The clones were then used for drug resistance study in pairs (i.e.
> clone treated vs clone untreated). I would like to ask you:
> 1. whether it is possible to do this kind of analysis (we mostly need
> copy number changes in the pairs) using aroma.affymetrix and and the
> cbs model built in your package?
Yes, you can use the Aroma framework to get CN segmentation results
based on CBS.
> 2. which parts of aroma.affymetrix I should use (i.e. how would you do
> it yourself?)
For getting CBS output, see the many examples on
http://www.aroma-project.org/. To segment CN ratios for tumor treated
vs non-treated, have a look at vignette 'Paired total copy-number
analysis' [http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis]
where you treat the non-treated as the reference (the "paired normals"
in that vignette).
> 3. is having the tumor and not the normal reference a big problem in
> this analysis - would the outcome be reliable?
If you're looking for differences between two DNA extracts (in your
case treated and non-treated matched tumor DNA, in other cases tumor
and matched normal DNA), the above approach will find such
differences.
> 4. I did the doCRMAv2() on them. Should I treat the two cell lines
> separately when applying doCRMAv2()?
No, because doCRMAv2() processes each array independently of the other
arrays in the data set - so it would not make a difference, cf.
http://aroma-project.org/blocks/doCRMAv2
Cheers,
Henrik
>
> Kind regards,
>
> Marcin
>
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version of the package, 2) to report the output of sessionInfo() and
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