Hi Liu, That is good to know some one is doing similar stuff as mine.
I was going to through 2-3 papers which described to get a comprehensive list of CNVs it is better to consider a CNV which is called in 2 or more CNV calling algorithms. This is what I have observed recently in some papers too. Please let me know if you want link for the papers I am talking about. I currently do not have them but will email you links for the papers. On Tuesday, January 20, 2015 at 5:01:46 PM UTC+1, Chengyu Liu wrote: > > 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/ > <http://www.google.com/url?q=http%3A%2F%2Faroma-project.org%2Fvignettes%2FpairedTotalCopyNumberAnalysis%2F&sa=D&sntz=1&usg=AFQjCNFXCJHW_UqojQMDh5FW1xbPLguBPA> > I was actually thinking about this. Wow this solves my problem. Thanks a lot mate for this information. > > > > 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. > I am lost here. Is there difference between CNA and CNV? > 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. >>>> >>>> >>>> Best Regards, 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.
