Hi, it's not easy to say. My point is that you look at the normal data, i.e. BAF (but also TCN relative to a global reference), you may have more clues on the quality of the normal sample. If that is bad, then then tumor-normal TCN is most likely bad too.
/Henrik On Tue, Feb 24, 2015 at 7:42 AM, Chengyu Liu <chengyu.liu...@gmail.com> wrote: > I understand DH is defined only for heterozygous SNPs. But the total copy > number estimates look ok. Do you think I need to discard this sample or not > when I do total copy number analysis? I will discard this sample when I do > parent-specific analysis. But not sure whether I should leave this sample > out for alteration calls. > > You are expert of PSCBS, can you give me suggestion here? > > Br, > C.Y > > On Monday, February 23, 2015 at 9:54:47 PM UTC+2, Henrik Bengtsson wrote: >> >> Hi, >> >> DH signals are only defined for heterozygous SNPs, so lack of DHs >> indicates a problem with the matched normal BAFs (see my other email). >> >> /Henrik >> >> On Mon, Feb 23, 2015 at 1:53 AM, Chengyu Liu <chengyu...@gmail.com> wrote: >> > It is difficult for me to say whether it is failed or the normal sample >> > is >> > nose. Can you have a look at these four figures ? They are from two >> > paired >> > tumor samples. One of them is missing DH . In the other sample, minor cn >> > is >> > 0 and major cn is 1. I am also attaching the total copy number estimate. >> > >> > Br, >> > Chengyu >> > >> > On Wednesday, February 18, 2015 at 11:25:48 PM UTC+2, Henrik Bengtsson >> > wrote: >> >> >> >> DH is only defined from heterozygous SNPs. If you don't see any DH >> >> signals, that indicates that none of the SNPs where called >> >> heterozygous. This could be an indicatation of a failed or a very >> >> noise normal sample. >> >> >> >> /Henrik >> > >> > -- >> > -- >> > 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-af...@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-affymetr...@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. -- -- 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.
