'Logicle' c++ class and its member functions are defined in 'logicle.h' and 'logicle.cpp' (from original author Wayne Moore), apparently you can use it in your c++ codes as long as you place the copyright notice ( see example file 'hyperlog.notice.html' in the flowCore source root). Here is how to use in c++: vector<double> output (n); Logicle lg = Logicle(T, W, M, A); for (int i = 0; i < n; i++)output[i] = lg->scale(output)[i] * M ; And Here is the R code for using logicle transformation data(GvHD) samp <- GvHD[[1]] ## User defined logicle function lgcl <- logicleTransform( w = 0.5, t= 10000, m =4.5) after <- transform(samp, `FL1-H` = lgcl(`FL1-H`), `FL2-H` = lgcl(`FL2-H`)) ## check the transformed results by plotting it densityplot(~`FL1-H`, samp) densityplot(~`FL1-H`, after) ## Automatically estimate the logicle transformation based on the data lgcl <- estimateLogicle(samp, channels = c("FL1-H", "FL2-H", "FL3-H", "FL2-A", "FL4-H")) ## transform parameters using the estimated logicle transformation after <- transform(samp, lgcl) ## plot all channels to check the transformed results densityplot(~., samp) densityplot(~., after) Mike On 04/14/2014 12:34 AM, Elina.Alaterre at horiba.com wrote: > Hi Mike, > > > I have cytometer data with coordinates for each point. These data were > compensated with Spillover matrix. > > How can I tranform these compensated data ? (I use my own C++ program to do > that) > > I find in the flowCore package some C++ scripts (logicleTransform.cpp, > Logicle.cpp, biexponential.c ...) I do not understand their features. Can > I use them to do the transformation ? > > If you have some tutorials. > > Also, when I use R to tranform data with the logicle transformation, I > would like to know the functions or methods used step by step. > > Sincerely, > Elina Alaterre. > > > >