Hi. On Fri, May 16, 2014 at 1:23 AM, Farhan Haq <farhanh...@gmail.com> wrote: > Hello, > > I have two questions regarding cnv analysis using CytoscanHD data. > > 1) > > I am currently implementing PSCBS on my Cancer datasets. This tool looks > quite interesting to me. > > However, what to do you say about giving exact values for calling copy > number gains and losses? Can you suggest any thresholds? Any values above 4 > would be high copy gains and near zero would be deletions?
Unfortunately, it does not work to call CN states by predetermined thresholds. The thresholds are sample specific and depends on such things as normal contamination, tumor heterogeneity and artificial compression introduced by the assay/technology. Calling CN states is very hard and I still haven't seen a caller that works satisfactory. > > I have a dataset of more than 200 hundred lung cancer samples so I want to > apply significant testing on cnvs. Does GISTIC type algorithms will work on > the attached example file? Or any other method you suggest I don't remember the details on GISTIC and what file format it accepts. What I know is that output format of PSCBS was *not* specifically designed to work with GISTIC, so it may or may not work out of the box. Otherwise, it shouldn't be too hard for someone who knows a little bit of programming to transform the file to something that GISTIC understands. > > > 2) > > Is tumorboost works with cytoscanHD data? Yes - TumorBoost can normalize any matched tumor-normal CN data regardless of chip type. Hope this helps Henrik > > Thanks > > -- > -- > 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.
