compensate-methods: Compensate a flowPlate to correct for the effects of...

Description Usage Arguments Value Author(s) See Also Examples

Description

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.

Usage

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## S4 method for signature 'flowPlate,ANY'
compensate(x, spillover)

Arguments

x

A flowPlate

spillover

The compensation matrix where the row and column names match the fluorescence channels of the flowPlate.

Value

Returns a compensated flowPlate.

Author(s)

Errol Strain

See Also

See Also compensation-class

Examples

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library(plateCore)
data(plateCore)

# Create the compensation matrix
comp.mat <- spillover(x=compensationSet,unstained=sampleNames(compensationSet)[5],
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)

plateCore documentation built on Nov. 1, 2018, 2:05 a.m.