R CGH IX: Aroma III

Next you will use the results from the previous step and perform CBS segmentation.

• To setup the model use the function CbsModel(), the parameter is the result from your previous analysis with doCRMAv2(), store your results in a valiable names sm.
• To run the segmentation use the function fit(sm, verbose=-10 ), this takes 10-15 minutes.

Visualization

Next step is to perform illustrate the Copy Number Profiles for the tumors.

• First you will link the ChromosomeExplorer to the segmentation model, this is done using the function ce <- ChromosomeExplorer(sm)
• Then to fit the model for all chromosomes, run:

process(ce, verbose=verbose)

• This takes about as long time as the doCRMAv2 analysis, to reduce the time you can do the analysis only for chromosomes 3 and 13, by adding the argument chromosomes = c(3,13) to the function.

• This command may result in the following error message:

ERROR caught in onFit.CopyNumberSegmentationModel():
<simpleError in png(..., type = "cairo"): unable to start device 'png'>

• don´t need to worry about this message, the analysis works anyway.
• Even before the analysis is finished you can start to see the results. Browse to the folder reports\GEO2\ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired and open the file ChromosomeExplorer.html in a webbrowser.

5. Hand in and compare the plots of chromosome 13 for the different samples.

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