In the PSCBS package, we provide the `estimateKappa()` function for estimating kappa, which we refer to as "background signal", cf. https://cran.r-project.org/web/packages/PSCBS/vignettes/PairedPSCBS.pdf. The kappa parameter is strongly correlated with the amount of normal contamination. We're very conservative in claiming it equals the normal contamination, because in order for that to be an accurate estimator we need to assume strong linearity in signals, which we don't want to claim. This is also why we keep 'kappa' somewhat under the radar. However, if you ignore this, you can treat kappa as an estimator for amount of normal contamination (others do that in other methods). In addition, it's pretty safe to say that kappa preserves the rank of the true normal contamination, that is, you can fairly safely compare kappa between samples and conclude that one sample has more normal contamination that another. What you cannot say for sure is the exact amount, which might be important when your trying to use it to control mutation rates etc.
Hope this helps Henrik On Fri, Apr 22, 2016 at 11:47 AM, Kevin McCormick <kevin.patrick.mccorm...@gmail.com> wrote: > Is there a way to incorporate tumor purity estimates (e.g. from ASCAT) into > the Aroma pipeline for segmenting copy number changes between parent and > tumor? We are looking at cell lines derived from tumors to compare > consistency between copy number variations. The tumor purity in the > parental cells has moderate variation, and the lines with lower purity in > the parental are getting called to have more copy number changes than those > with higher purity, even though a manual inspection suggests the differences > are merely due to change in purity. > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
