Hi Liu,
On Wednesday, January 21, 2015 at 4:21:04 PM UTC+1, Chengyu Liu wrote: > > 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~! > I have tried this and works good but at the end I need the information whether there is a gain or loss at the segment. I will use GLAD model to get gain or loss at a segment. My samples and controls are completely unrelated so I am little bit doubtful whether I am doing right or not. I also found some other algorithms that can work on segments produced by CBS model still looking into them. > > >> >>> >>> >>> 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. > Then I am also looking for CNA. What other softwares have you tried on data from CytoScan HD array? > > >> >> >> >>> 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. >> > 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. 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