Could be a sample annotation mistake. Wouldn't be the first time it happened.
On Thu, Mar 5, 2015, 01:34 Chengyu Liu <chengyu.liu...@gmail.com> wrote: > You might be right. The BAF of the normal sample is strange if the way I > check is correct. I checked the how many bands there are. Normally there > are three but there are only two bands in the normal sample(see > attachment). The tumor sample looks okey. > > > Br, > Chengyu > > > On Wednesday, February 25, 2015 at 10:36:10 PM UTC+2, Henrik Bengtsson > wrote: > >> 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...@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-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. 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