plateCore (version 1.30.0)

fixAutoFl: Correct for the effects of cell size (FSC) on autofluorescence

Description

The fixAutoFl function uses the method of Hahne et al. 2006 (Genome Biology) to fit a robust, log-log linear regression to the fluorescence channel of interest versus forward scatter (FSC). The current implementation scales the corrected data so the median fluorescence intensity (MFI) is the same before and after fixAutoFl.

Usage

fixAutoFl(fp,fsc="FSC.A",chanCols,unstain,...)

Arguments

fp

A flowPlate

chanCols

Selected channels to correct for autofluorescence.

unstain

Name(s) of the unstained samples. The function will try to find samples with Sample.Type="Unstained" if no names are given. If there are multiple unstained samples the function will average the slopes.

fsc

Name of the FSC parameter.

...

optional arguments

Value

Returns a flowPlate with autofluorescence due to cell size (FSC) corrected.

Examples

library(plateCore)
data(plateCore)

## Get the lymphocytes
rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400))
pbmcPlate <- Subset(pbmcPlate, rectGate)

## Create a flowPlate object from the platePBMC and the wellAnnotation
fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")

## Correct for autofluorescence in FL1.H-FL4.H
fp <- fixAutoFl(fp,fsc="FSC-H",chanCols=c("FL1-H","FL2-H","FL3-H","FL4-H"))