Hi, > 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. > >> >> I think you can use GLAD to call gain and loss. But CBS does not return gain or loss, only segments. If you use CBS you should call gain or loss yourself (or use other tools such as GISTIC).
> Then I am also looking for CNA. What other softwares have you tried on > data from CytoScan HD array? > Like you I used aroma to preprocess, segmented using CBS and manually call gain or loss. The simplest way is using a threshold to define gain or loss. If I remember correctly, one of TCGA papers in Nature, there a fixed threshold was used to define gain and loss. Maybe you can check that. Br, >> >>> >>> >>> >>>> 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. 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.
