CORRECTION: ref.theta <- extractMatrix(Normal) theta <- extractMatrix(Tumor) C <- 2 * theta/ref.theta
On Mon, Dec 12, 2011 at 1:09 PM, Gregory W <greg.d.w...@gmail.com> wrote: > 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/
