Hi Sam, I am doing similar stuff with you. I also need to identify regions which are amplified or deleted. I have paired samples. There are quite many different ways to define gain and loss of a segment. It is a tricky question.
>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. > I did not get your point. > When I tried GLAD on just 3 samples, it took more than 30 minutes to > finish. > My experience is that CBS is faster than GLAD. When I ran GLAD with 4 samples, it took like two or more to finish them. > > 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. > You can replace GLAD model with CBS model (cns <- CbsModel(dsT, dsN)where dsN is average of all the controls). http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis/ Do you need to identify copy number alterations (CNA)? or Just copy number variants(CNV)? I need to identify CNA not CNV. For now I do not know how. Do you know also how to map amplified or deleted region to genes? If you know something about it, happy to hear. Br, C.Y > > 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 firstname.lastname@example.org 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.