Hi Chengyu, On 4 February 2015 at 15:45, Chengyu Liu <chengyu.liu...@gmail.com> wrote:
> Thanks Sam for sharing the information. > But I dont understand, why there are chromosome 24 and 25 (autosomal > chromosome 1-22, X(23), Y(24))? > yes, 23 is chromosome X and 24 is chromosome Y. Chromosome 25 is for pseudo-autosomal regions in X. Are you using any other package than aroma.affymetrix ? > Yes, I am using ChAS to find CNAs. > Are you interested in total copy number or allele-specific copy number > analysis ? > I am interested in allele-specific copy number analysis. > > Now I am working on allele-specific copy number analysis. But I am stuck > in the steps where copy number alterations are called and LOHs are > identified. Do you have any suggestions? > ChAS actually does lot analysis along with calling CNV. LOH is one of them. Probably it is better if you can use that. > How about you ? > We are not yet concerned about LOH till now. Maybe in future. > > Br, > C.Y > > On Wednesday, February 4, 2015 at 10:37:46 AM UTC+2, Sam Padmanabhuni > wrote: >> >> HI Chengyu, >> >> Yes, I do have chromosome 23, 24 and 25. We are only interested in CNAs >> in autosomal chromosomes so not going to include X and Y chromosomes in >> further analysis. >> >> Best, >> Sam. >> >> >> On 4 February 2015 at 10:31, Chengyu Liu <chengyu...@gmail.com> wrote: >> >>> Hi Sam, >>> >>> I would like to discuss something about cytoscanHD array. Did you find >>> that when you have done preprocessing, there are chromosome 24 and 25 ? >>> >>> Br, >>> Chengyu >>> >>> -- >>> -- >>> 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 a topic in the >>> Google Groups "aroma.affymetrix" group. >>> To unsubscribe from this topic, visit https://groups.google.com/d/ >>> topic/aroma-affymetrix/wCFGrViNri4/unsubscribe. >>> To unsubscribe from this group and all its topics, 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 a topic in the > Google Groups "aroma.affymetrix" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/aroma-affymetrix/wCFGrViNri4/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > Best, Sam. -- -- 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.
