flowCore: inverse logicle transformation of flow cytometry data
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@spynebroadinstituteorg-3685
Last seen 7.3 years ago
Hi, Wondering if the inverse function of logicle was implemented. Thanks, -Pyne Quoting Chao-Jen Wong <cwon2 at="" fhcrc.org="">: > Hi, Pyne, > > I agree with you that it is good to have an inverse function. Thanks for > your suggestion and tips. We will try to implement it next week. > > Thanks, > Chao-Jen > > spyne at broadinstitute.org wrote: >> >> Hi, >> >> The reason I need the inverse function for logicle is because >> after I have computationally identified the cluster of events in >> logicle-transformed marker space, now I want to use the knowledge >> of that range of events in the original, untransformed scale for >> sorting out similar events in the subsequent experiments. >> >> My guess is that this may not be a very far-fetched scenario, >> and since the transformation is deterministic and bijective >> anyway, an inverse function would be good to have, at least for >> the default argument settings. One option is of course a slow >> numerical computation method. >> >> However, since the transformation is monotonic, for a fixed setting >> of arguments (e.g. the default setting), doing a simple binary search >> over a reasonable range is a cheap way to approximate the inverse >> within a desirable accuracy. >> >> Thanks! >> -Pyne >> >> >> Quoting Chao-Jen Wong <cwon2 at="" fhcrc.org="">: >> >>> Hi, Pyne >>> >>> That is an interesting question. flowCore does not have an inverse >>> function for the logicle transformation. Since the logicle >>> transformation is an one-to-one and onto function, it is possible to >>> implement an inverse function. It is, however, not straightforward. Do >>> you really really need such a function? >>> >>> spyne at broadinstitute.org wrote: >>>> >>>> Hi, >>>> >>>> I applied logicle transformation (with default arguments) >>>> to my data points, then detected the subpopulations of >>>> interest in the transformed data, and now I want to >>>> revert the subpopulations back to the original scale of >>>> the untransformed state. >>>> >>>> In other words, if I want to apply the inverse of the logicle >>>> transformtion (applied with default arguments, which I do not >>>> know) to my data, is that possible? >>>> >>>> Thanks. >>>> -Pyne >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> Chao-Jen Wong >>> Program in Computational Biology >>> Division of Public Health Sciences >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Avenue N., M2-B876 >>> PO Box 19024 >>> Seattle, WA 98109 >>> 206.667.4485 >>> cwon2 at fhcrc.org >>> >>> >> >> > > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M2-B876 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2 at fhcrc.org > >
Cancer flowCore Cancer flowCore • 512 views
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@nishant-gopalakrishnan-3253
Last seen 7.3 years ago
Hi Pyne, I am working on a function to calculate the inverse and will be checking in some changes today. Thanks in advance for your patience. Nishant spyne at broadinstitute.org wrote: > > Hi, > > Wondering if the inverse function of logicle was implemented. > > Thanks, > -Pyne > > > Quoting Chao-Jen Wong <cwon2 at="" fhcrc.org="">: > >> Hi, Pyne, >> >> I agree with you that it is good to have an inverse function. Thanks for >> your suggestion and tips. We will try to implement it next week. >> >> Thanks, >> Chao-Jen >> >> spyne at broadinstitute.org wrote: >>> >>> Hi, >>> >>> The reason I need the inverse function for logicle is because >>> after I have computationally identified the cluster of events in >>> logicle-transformed marker space, now I want to use the knowledge >>> of that range of events in the original, untransformed scale for >>> sorting out similar events in the subsequent experiments. >>> >>> My guess is that this may not be a very far-fetched scenario, >>> and since the transformation is deterministic and bijective >>> anyway, an inverse function would be good to have, at least for >>> the default argument settings. One option is of course a slow >>> numerical computation method. >>> >>> However, since the transformation is monotonic, for a fixed setting >>> of arguments (e.g. the default setting), doing a simple binary search >>> over a reasonable range is a cheap way to approximate the inverse >>> within a desirable accuracy. >>> >>> Thanks! >>> -Pyne >>> >>> >>> Quoting Chao-Jen Wong <cwon2 at="" fhcrc.org="">: >>> >>>> Hi, Pyne >>>> >>>> That is an interesting question. flowCore does not have an inverse >>>> function for the logicle transformation. Since the logicle >>>> transformation is an one-to-one and onto function, it is possible to >>>> implement an inverse function. It is, however, not >>>> straightforward. Do >>>> you really really need such a function? >>>> >>>> spyne at broadinstitute.org wrote: >>>>> >>>>> Hi, >>>>> >>>>> I applied logicle transformation (with default arguments) >>>>> to my data points, then detected the subpopulations of >>>>> interest in the transformed data, and now I want to >>>>> revert the subpopulations back to the original scale of >>>>> the untransformed state. >>>>> >>>>> In other words, if I want to apply the inverse of the logicle >>>>> transformtion (applied with default arguments, which I do not >>>>> know) to my data, is that possible? >>>>> >>>>> Thanks. >>>>> -Pyne >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> -- >>>> Chao-Jen Wong >>>> Program in Computational Biology >>>> Division of Public Health Sciences >>>> Fred Hutchinson Cancer Research Center >>>> 1100 Fairview Avenue N., M2-B876 >>>> PO Box 19024 >>>> Seattle, WA 98109 >>>> 206.667.4485 >>>> cwon2 at fhcrc.org >>>> >>>> >>> >>> >> >> >> -- >> Chao-Jen Wong >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., M2-B876 >> PO Box 19024 >> Seattle, WA 98109 >> 206.667.4485 >> cwon2 at fhcrc.org >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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