flowCore: logicle transformation of flow cytometry data
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@saumyadipta-pyne-3343
Last seen 7.3 years ago
Hi, I am doing some simulations on flow experiments, and therefore the data are just a plain numerical matrix of fake scatter and marker readouts. Thus, the data are not read with read.FCS nor saved as a flowFrame. Instead I save the matrix as a data frame (call it Ab). The data, generated by me, have all entries present and containing integral (real) values. When I try to apply the logicle transformation to the data, it shows the following error: > ltr=logicleTransform("logicle") > transform(Ab, "logicle.Ab1"=ltr(Ab1)) > Error in ltr(Ab1) : Input must be real values. However I do not get any error with, say, truncateTransform. Is there a domain of real values for which logicle is not defined? Please let me know what I might be doing wrong above. Thanks. -Pyne
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@nishant-gopalakrishnan-3253
Last seen 7.3 years ago
Hi Pyne Its giving you an error because, the C function implementing the logicle transform is doing some type checking to see if the data supplied to it is a real number. for example , ltr=logicleTransform("logicle") ltr(c(1:10)) ## would give you an error as class(c(1:10)) is "integer" ltr(as.real(c(1:10))) ## would work as the input is a real number Nishant Saumyadipta Pyne wrote: > Hi, > > I am doing some simulations on flow experiments, and therefore the > data are just a plain numerical matrix of fake scatter and marker > readouts. Thus, the data are not read with read.FCS nor saved as > a flowFrame. Instead I save the matrix as a data frame (call it Ab). > > The data, generated by me, have all entries present and containing > integral (real) values. When I try to apply the logicle transformation > to the data, it shows the following error: > > > ltr=logicleTransform("logicle") > > transform(Ab, "logicle.Ab1"=ltr(Ab1)) > > Error in ltr(Ab1) : Input must be real values. > > However I do not get any error with, say, truncateTransform. > Is there a domain of real values for which logicle is not defined? > Please let me know what I might be doing wrong above. > > 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
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Hi Pyne, Nishant, I think the R wrapper should coerce the input to numeric. Integer values aren't that uncommon in flow data, although in a flowFrame they will always be stored as floating points. To most R users the notion of data types is not that relevant (after all, R automatically coerces in most cases), and this seems to be one of the places where a slightly more intelligent software doesn't hurt. Florian Quoting Nishant Gopalakrishnan <ngopalak at="" fhcrc.org="">: > Hi Pyne > > Its giving you an error because, the C function implementing the logicle > transform is doing some type checking to see if the data supplied to it > is a real number. > for example , > ltr=logicleTransform("logicle") > ltr(c(1:10)) ## would give you an error as class(c(1:10)) is "integer" > > ltr(as.real(c(1:10))) ## would work as the input is a real number > > Nishant > > Saumyadipta Pyne wrote: >> Hi, >> >> I am doing some simulations on flow experiments, and therefore the >> data are just a plain numerical matrix of fake scatter and marker >> readouts. Thus, the data are not read with read.FCS nor saved as >> a flowFrame. Instead I save the matrix as a data frame (call it Ab). >> >> The data, generated by me, have all entries present and containing >> integral (real) values. When I try to apply the logicle transformation >> to the data, it shows the following error: >> >> > ltr=logicleTransform("logicle") >> > transform(Ab, "logicle.Ab1"=ltr(Ab1)) >> > Error in ltr(Ab1) : Input must be real values. >> >> However I do not get any error with, say, truncateTransform. >> Is there a domain of real values for which logicle is not defined? >> Please let me know what I might be doing wrong above. >> >> 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 > > _______________________________________________ > 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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