Hi. On Mon, Apr 30, 2012 at 5:31 AM, Marcin <kke...@gmail.com> 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 > > -- > 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 website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- 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 website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
