LRR are basically log2 CN ratios centered around 0 whereas CT are non-logged CN ratios centered around 2 (or whatever you think the ploidy is), so CT = 2^LRR should do.
/H On Tue, Sep 18, 2012 at 6:28 AM, Reed <ghosh...@gmail.com> wrote: > I am trying to run segmentByPairedPSCBS on my illumina 1M dataset. This R > function require CT parameter - which is a A numeric vector of J tumor total > copy number (TCN) ratios in [0,+Inf). I am unable to get anything apart from > BAF and LRR from Genomestudio output. How I can estimate CT from my data ? > > Thanks > Reed > > -- > 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/
