Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi Sam, I would like to discuss something about cytoscanHD array. Did you find that when you have done preprocessing, there are chromosome 24 and 25 ? Br, Chengyu -- -- 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.
Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
Thanks Sam for sharing the information. But I dont understand, why there are chromosome 24 and 25 (autosomal chromosome 1-22, X(23), Y(24))? Are you using any other package than aroma.affymetrix ? Are you interested in total copy number or allele-specific copy number analysis ? Now I am working on allele-specific copy number analysis. But I am stuck in the steps where copy number alterations are called and LOHs are identified. Do you have any suggestions? How about you ? Br, C.Y On Wednesday, February 4, 2015 at 10:37:46 AM UTC+2, Sam Padmanabhuni wrote: HI Chengyu, Yes, I do have chromosome 23, 24 and 25. We are only interested in CNAs in autosomal chromosomes so not going to include X and Y chromosomes in further analysis. Best, Sam. On 4 February 2015 at 10:31, Chengyu Liu chengyu...@gmail.com javascript: wrote: Hi Sam, I would like to discuss something about cytoscanHD array. Did you find that when you have done preprocessing, there are chromosome 24 and 25 ? Br, Chengyu -- -- 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-af...@googlegroups.com javascript: To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to a topic in the Google Groups aroma.affymetrix group. To unsubscribe from this topic, visit https://groups.google.com/d/topic/aroma-affymetrix/wCFGrViNri4/unsubscribe . To unsubscribe from this group and all its topics, send an email to aroma-affymetr...@googlegroups.com javascript:. For more options, visit https://groups.google.com/d/optout. -- -- 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.
[aroma.affymetrix] Re: Regarding the copy number states and further processing
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.
Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi guys, here are some late feedback on this discussion: * When talking about copy numbers, it is important to always be very clear and distinguish between whether we talk about normal/germline CNs or tumor CNs. The former take integer CN levels (0, 1, 2, 3, ...), whereas for tumors we very rarely observe pure homogeneous tumor cells, which is why we only measure and observe non-integer CN levels. Hopefully, we observe at least discrete CN levels in tumors, but one should never expect integer levels. * aCGH: a historical term often used as a synonym for total copy numbers. For example, some say aCGH analysis when they really mean total copy-number analysis. aCGH stands for array-CGH, or in full 'array comparative genomic hybridization'. This refers to the older generation two-color/two-channel arrays where a test and a reference sample where labelled with two different dyes and competitively hybridized to the same array and the same probes. I recommend to stop using this term and instead use total copy number, total CN, or TCN (when it's clear). By being explicit about total, you're also explicitly contrasting it to parent-specific CNs (which you can do if you have SNP data). * CNA: Copy-Number Aberration. This term can be applied to both tumor and germline samples. In tumors you expect non-integer CN levels. In germline/normals you expect integer CN levels (0, 1, 2, 3, ...). * CNP: Copy-Number Polymorphism. This term applies to copy-number differences in relationship to a population. This also implies we're talking about germline genomes. In other words, CNPs are also integer CN levels (0, 1, 2, 3, ...). CNPs are used to specify, say, 2% of the Europeans have a 1 copy deletion of length 1.0-1.5 Mb on Chr 3 at 124.5Mb. CNPs is for segment deletions and gains what SNPs are for nucleotide polymorphisms. The term CNP is rare. It is much more common to hear/see CNV. * CNV: Copy-Number Variation. Ideally the word variation refers to polymorphism and therefore the term CNV should be used only to refer to CNPs. I don't know if there is a formal definitions, but I find it unfortunate to see CNV being used when CNA should be used. By my books, CNV only takes integer CN levels (0, 1, 2, 3, ...). The term CNV should never be used to refer to CN levels in tumors. * Calling total CN levels is very hard in tumors, and as the first above point alludes to, it may not even be a well defined problem. For instance, imagine you have a tumor sample with 5% tumor cells and 95% normal cells, and that the those tumors cells all have a deletion on Chr 2. Then, at what point to you consider that sample itself to have a deletion on Chr 2? Are you after he sample/tissue itself, or are you after those 5% tumors cells? What if you have a heterogeneous mix of tumor cells? The more precise you can specify your question the more easy it is for you to decided what approach forward (may) work and what doesn't work. Here work can also be read as make sense. * The first and most important task for almost all segmentation methods is to *segment* the genome, that is, identify at what genomic locations the observed DNA (tumor, normal or a mix) changes in CN level. Together, these location, aka change points, defines how the genome can be partitioned into segments with equal CN levels, such that when we look at a particular segment, we can assume that all genomic locations within that segment has the same underlying genomic composition (e.g. gain, loss, loss in 5% of the cells, etc.). CBS, GLAD, and many other methods, segment the genome this way as a first step. * A common task after having decided on the segments (partitioning of the genome), is to decide on what is going on within each segment. Not all methods does this. For instance, CBS only provides you with the change points. GLAD on the other hand does both the segmentation and then also provides a method for calling. Theoretically, there is nothing preventing you from using the GLAD *calling* algorithm using the segmentation found by CBS. Unfortunately, I don't think it is straightforward to do that in practice; at least you have to coerce one data format into one that GLAD understands. * GLAD does not scale well with the number of loci, because it's computational complexity is ~O(n^2), unless things have changed since. In 2007, I tried to predict GLAD's processing time when we were using the Affymetrix 500K chips and the GenomeWideSNP_5 and GenomeWideSNP_6 were starting to come out. A GWS6 chip would basically take days to segment. See attached PNG for a table. * CBS is much faster as an algorithm. Also, the implementation in the DNAcopy package has been made even faster over time. There was a major speedup back in 2009, cf. http://aroma-project.org/benchmarks/DNAcopy_v1.19.2-speedup/ Over and for now Henrik On Thu, Jan 22, 2015 at 12:42 AM, Chengyu Liu chengyu.liu...@gmail.com wrote: Hi, I have tried this and works good but at the
[aroma.affymetrix] Re: Regarding the copy number states and further processing
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%2Fsa=Dsntz=1usg=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
[aroma.affymetrix] Re: Regarding the copy number states and further processing
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%2Fsa=Dsntz=1usg=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. To unsubscribe from this group and stop receiving emails from it, send an email to
[aroma.affymetrix] Re: Regarding the copy number states and further processing
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 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.
[aroma.affymetrix] Re: Regarding the copy number states and further processing
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%2Fsa=Dsntz=1usg=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.
[aroma.affymetrix] Re: Regarding the copy number states and further processing
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 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.
[aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi, Thanks for the clarification. I am working on finding segments of duplication/deletion that are only present in patients but not in controls. And my samples are non-paired. 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. When I tried GLAD on just 3 samples, it took more than 30 minutes to finish. 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. 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 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.
