Flow samples are often stained with multiple types of fluorophores. Unfortunately, the emission spectra for these different fluorophores often overlap, and the signals must be corrected before proceeding with the analysis. Compensate adjusts for spillover using the method implemented in the package flowCore. Unlike flowCore, compensate only adjusts for the dyes/fluorophores listed in wellAnnotation.
## S4 method for signature 'flowPlate,ANY' compensate(x, spillover)
The compensation matrix where the row and column names match the fluorescence channels of the flowPlate.
Returns a compensated
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library(plateCore) data(plateCore) # Create the compensation matrix comp.mat <- spillover(x=compensationSet,unstained=sampleNames(compensationSet), patt=".*H",fsc="FSC-H",ssc="SSC-H",method="median") ## Get the lymphocytes rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400)) pbmcPlate <- Subset(pbmcPlate, rectGate) # Create a flowPlate from the sample data in plateCore fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1") # apply the compensation matrix fp <- compensate(fp,comp.mat)
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