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 > <javascript:>> 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 > <javascript:> > > 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 <javascript:>. > > 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.
