calcPBChiSquare: Probability binning metirc for comparing the probability...
In flowStats: Statistical methods for the analysis of flow cytometry data

Description Usage Arguments Value Author(s) See Also Examples

This function calculates the Probability binning metric proposed by Baggerly et al. The function utilizes the data binned using the proBin and binByRef functions.

1	calcPBChiSquare(ctrlRes,sampRes,ctrlCount,sampCount)

`ctrlRes`	The result generated by calling the `probBin` function on a control dataset.
`sampRes`	The result generated by calling the `byByRef` function on a test sample dataset
`ctrlCount`	The number of events in the control sample
`sampCount`	The number of events in the test sample being compared

A list containing the statistic, p.value, observed, expected counts and the residuals

Nishant Gopalakrishnan

proBin, calcPBChiSquare

library(flowCore)
data(GvHD)
# flow frame 1 is treated as  control dataset and used to generate bins
resCtrl<-proBin(GvHD[[1]][,c("FSC-H","SSC-H","Time")],200)  
plotBins(resCtrl,GvHD[[1]],channels=c("FSC-H","SSC-H","Time"),title="Binned control data")
# Same bins are applied to flowFrame 16
resSample<-binByRef(resCtrl,GvHD[[16]][,c("FSC-H","SSC-H","Time")])
ctrlCount<-nrow(GvHD[[1]])
sampCount<-nrow(GvHD[[16]])
stat<-calcPBChiSquare(resCtrl,resSample,ctrlCount,sampCount)