Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi Chengyu, On 4 February 2015 at 15:45, Chengyu Liu wrote: > 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))? > yes, 23 is chromosome X and 24 is chromosome Y. Chromosome 25 is for pseudo-autosomal regions in X. Are you using any other package than aroma.affymetrix ? > Yes, I am using ChAS to find CNAs. > Are you interested in total copy number or allele-specific copy number > analysis ? > I am interested in 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? > ChAS actually does lot analysis along with calling CNV. LOH is one of them. Probably it is better if you can use that. > How about you ? > We are not yet concerned about LOH till now. Maybe in future. > > 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 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 >>> 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. >>> 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 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-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > 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
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 > 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 >> >> 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 . >> 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.
Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
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 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-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 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-affymetrix+unsubscr...@googlegroups.com. > 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.
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
Hi Henrik, Thank you very much for the information and it has clarified lot of my doubts. Best, Sam. On Thursday, January 22, 2015 at 8:36:59 PM UTC+1, Henrik Bengtsson wrote: > > 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 tak
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 wrote: > Hi, > >> >> I have tried this and works goo
