Hi, Thanks for the clarification.
I am working on finding segments of duplication/deletion that are only present in patients but not in controls. And my samples are non-paired. >From the literature search, it seems best to call CNVs using from different softwares to have a comprehensive list before doing association analysis. For this reason, I need to know gain or loss of DNA in a segment. When I tried GLAD on just 3 samples, it took more than 30 minutes to finish. I don't know how to incorporate this segments from CBS in to my analysis. Please let me know if you have any ideas on how to solve this. Thanks, Best Regards, Sam. On Tuesday, January 20, 2015 at 10:38:27 AM UTC+1, Chengyu Liu wrote: > > Hi, > > On Monday, January 19, 2015 at 3:42:59 PM UTC+2, Sam Padmanabhuni wrote: >> >> Dear AromaAffymetrix Team, >> >> First of all, thank you very much for such a detailed vignette on how to >> perform the CNV analysis. >> >> I am Sam, a PhD student in genetics, working on CNV analysis on data from >> CytoScan HD Array. I have read the vignette to do CRMAv2 and non-paired >> CBS. I have copied the commands and ran in R. >> >> But, I have few questions regarding CbsModel and GladModel in >> segmentation algorithm: >> >> 1. It is mentioned that, copy number states is not calculated in CbsModel >> segmentation. How do I get information of whether the segment is a loss or >> gain from output of CbsModel? I mean can this information be passed to >> other algorithms to estimate copy number state. >> > As far as I know, the out put of CBS is the relative copy number. It does > not directly tell you the copy number states. > >> >> 2. I have looked in to GLAD model and it is mentioned that it is >> developed for aCGH but my data is not from aCGH. Can it be still used to >> calculate copy number states for the data I am working on? >> > GLAD can calculate copy number states for affy-array, although I have not > used it before. > >> >> 3. Also, do you have a vignette on how to run CRMAv2 and CBS on CytoScan >> HD array? This would be really helpful. >> > It is the same with other chiptype, prepare input as required (there is > vignette). > > > BTW, I am also working on CytoScan HD. What kind of analysis are you going > to do? Do you have paired samples or non-paired? Maybe we have something > common and we can discuss. > > Br, > C.Y > > > >> Thank you, >> >> 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.
