spillover {flowCore}R Documentation

Compute a spillover matrix from a flowSet

Description

Spillover information for a particular experiment is often obtained by running several tubes of beads or cells stained with a single color that can then be used to determine a spillover matrix for use with compensate.

Usage

## S4 method for signature 'flowSet':
spillover(x, unstained = NULL, patt = NULL, fsc = "FSC-A", 
        ssc = "SSC-A", method = "median")

Arguments

x A flowSet of compensation beads or cells
unstained The name of index of the unstained negative control
patt An optional regular expression defining which parameters should be considered.
fsc The name or index of the forward scatter parameter
ssc The name or index of the side scatter parameter
method The statistic to use for calculation. Traditionally, this has been the median so it is the default. The mean is sometimes more stable.

Details

The algorithm used is fairly simple. First, using the scatter parameters, we restrict ourselves to the most closely clustered population to reduce the amount of debris. The selected statistic is then calculated on all appropriate parameters and the unstained values swept out of the matrix. Every sample is then normalized to [0,1] with respect to the maximum value of the sample, giving the spillover in terms of a proportion of the primary channel intensity.

Value

A matrix for each of the parameters

Author(s)

B. Ellis

References

C. B. Bagwell & E. G. Adams (1993). Fluorescence spectral overlap compensation for any number of flow cytometry parameters. in: Annals of the New York Academy of Sciences, 677:167-184.

See Also

compensate


[Package flowCore version 1.0.2 Index]