Hi, Sam, No thanks, I don't need the reference papers.
On Tuesday, January 20, 2015 at 6:52:42 PM UTC+2, Sam Padmanabhuni wrote: > > 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. > Excellent~! > >> >> >> 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? > But I am sure there are different. CNA refers to somatic copy number variants, and CNV refers to germline copy number variants. Once you have reference samples, the results you will get is CNA. > > > >> 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. 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