Hi Henrik, On this page http://aroma-project.org/vignettes/PairedPSCBS-lowlevel you showed how to make whole genome plots of TCN, the decrease-of-heterozygosity (DH), and the minor-major CN estimates. Is there a way to make such plots for individual chromosomes?
Thanks, Michelle On Fri, Feb 17, 2012 at 6:04 PM, Henrik Bengtsson <h...@biostat.ucsf.edu>wrote: > Hi, > > On Fri, Feb 17, 2012 at 1:44 PM, Michelle <suyi...@gmail.com> wrote: > > Hi Henrik, > > > > I ran the PSCBS package on some Affy SNP 6.0 arrays. In the output I > found > > that several files contain a few lines of negative "tcnMean" values, > while > > the rest are all positive. My question is - the total copy number is > > supposed to be positive, right? Are these negative values caused by some > > error in the computation? If so, how to adjust them? > > yes, *true*/*biological* CNs cannot be negative. However, > *observed*/*estimated* ones may very well end up being *slightly* > negative, due to noise in data. So, it is neither a bug nor something > wrong with PSCBS. > > There is nothing in Paired PSCBS that enforces the CNs to be strictly > non-negative (>= 0), neither does it restrict the CN estimates to be > integers (0, 1, 2, 3, ...), because there may be normal cell > contamination or tumor clonality. However, you can imagine that there > are downstream methods that takes the PSCBS estimates and make such > decisions, but that is not part of PSCBS itself. > > You can always manual adjust negative estimates to be zero, if you > really need them not to be negative, but I still haven't had to do it. > > /Henrik > > > > > Thanks, > > Michelle > > > > -- > > 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/ > -- 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/
