Hello, Many thanks for the site and quick feedback to the discussion board.
I was hoping to get a little clarification about the difference between these two statistics: Raw CN and CBS mean. After running CBS I get the following data frame: cbs <- CbsModel(tumor, normal, min.width=5, alpha = .01) fit(cbs, min.width=5, verbose=0, force=TRUE) regions <- getRegions(cbs) regions <- regions[[1]][,1:5] head(regions) chromosome start stop mean count 1 1 51599 25455929 0.0870 14665 2 1 25465716 25519534 -1.2750 29 *** 3 1 25519574 26308518 0.0994 369 4 1 26313794 27104892 0.4272 336 5 1 27108799 38042779 0.1022 6161 6 1 38044082 38063269 -0.6952 8 Where column "mean" is the result from DNAcopy segmentation for the particular region -- which is just the mean log-ratio-value of all probes in the region. And I'm assuming that since I ran doCRMAv2 on the data, the CBS code above is performed on normalized "tumor" and "normal" data. Focusing on regions 2 show above with trailing ***, if I run: ref.theta <- extractMatrix(ref.average) theta <- extractMatrix(file.group) C <- 2 * theta/ref.theta And then calculate the mean raw CN using matrix C for the same probes in regions 2 used to calculate the CBS mean of -1.2750: does this CN mean relate in any way to the CBS mean? I realize the log ratio is logged and centered around 0 for the segmented data, whereas, CN is around 2, but aside from simple transformations can you help me understand the difference between these two statistics? Does the mean CN for probes included in a particular CBS segmented regions have any value? Many thanks! Greg -- 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/
