flowBeads

This is the public repository for the flowBeads Bioconductor package for working with calibration beads in flow cytometry, based on flowCore.

flowBeads has received some recent attention, in particular I had a few questions about relative normalisation for channels in which the bead manufacturer does not specify the bead MEF.

I think relative normalisation is possible, provided that the number of peaks is consistent across samples. However I believe it is easier to achieve this without using the Bioconductor package which can be quite rigid and cumbersome.

Instead, here is some R code of how to go about it, which also makes use of flowClust for clustering on forward and side scatter in order to filter doublets:

require(flowCore)
# We will use cluster for the pam function (implementation of k medoids).
require(cluster)
# flowClust is a very useful Bioconductor package to do clustering by fitting a mixture of normal distributions.
# It also ignores outliers from the clustering.
require(flowClust)
# This package provides the download.file function.
# If download file doesn't work (returns status code 127) then you can just download the file and save it in the directory
# where you run the script.
require(RCurl)
# This is another repository of mine containing some plotting functions for flow data.
download.file("https://raw.githubusercontent.com/pontikos/FCS/master/fcs.R", destfile = "fcs.R", method = "curl")
source('fcs.R')

This function will retrieve the MFIs of the 8 bead populations:

get.MFI <- function(X) {
  print(length(scatter.channels <- as.character(grep('FSC|SSC',colnames(X),value=TRUE))))
  print(length(fluo.channels <- as.character(grep('^SSC|FSC|Time',colnames(X),invert=T,value=T))))
  # use PCA to reduce the number of dimensions from 6 to 2
  pca <- princomp(X[,scatter.channels])
  pca.X <- pca$scores[,1:2]
  #smoothPlot(pca.X)
  # This might not always be necessary depending.
  # A good way of finding out is to plot the FSC-A against SSC-A.
  res <- flowClust(pca.X,K=4)
  #plot to check result
  #plotClustRes(pca.X,res=res,outliers=FALSE)
  # Pick population which contains the most beads.
  X <- X[which(res@label==which.max(res@w)),]
  X.trans <- apply(X[,fluo.channels],2,logicleTransform())
  res <- pam(X.trans[,fluo.channels],8)
  #check results
  plotClusters(X.trans[,fluo.channels[1:4]],outliers=TRUE, classification=res$clustering,chulls=FALSE) 
  plotClusters(X.trans[,fluo.channels[4:8]],outliers=TRUE,classification=res$clustering,chulls=FALSE)
  # these are now the MFIs
  MFIs <-do.call('rbind',by(X[,fluo.channels],res$clustering,colMeans))
  MFIs <- MFIs[order(MFIs[,1]),]
  return(MFIs)
}

beads1 <- flowCore::read.FCS(file.path("lucas","QC8PeaksBeads_ After Capture Beads_SAS_ARIAIII_CORDOBA_19112014.fcs"))
MFI.beads1 <- get.MFI(beads1@exprs)
beads2 <- flowCore::read.FCS(file.path("lucas","QC8PeaksBeads_32140219_SAS_ARIA_19MAR2015_19MAR2015.fcs"))
MFI.beads2 <- get.MFI(beads2@exprs)

Next it's simply a question of defining the linear transforms which maps the peaks between samples:

fluo.channels <- colnames(MFI.beads1)
trans <-do.call('rbind', lapply( fluo.channels, function(chan) coefficients(lm(log10(MFI.beads1[,chan])  ~ log10(MFI.beads2[,chan]))) ) )
rownames(trans) <- fluo.channels
colnames(trans) <- c('alpha','beta')
# if beta is not an integer, this normalisation is only defined for positive x
# since beta is usually very close to 1 it may be worth just setting to 1
trans[,'beta'] <- 1
normalisation <- lapply(fluo.channels , function(n) return(function(x) 10**trans[n,'alpha'] + x**trans[n,'beta']) )
names(normalisation) <- fluo.channels

Now normalisation contains the transform to compare samples analysed on the same day as beads2 with those analysed at the same day as beads1. So for example if x contains your data from day 2 then you can simply do this to normalise it to day 1:

  chan <- 'APC-AF750-A'
  x <- beads2@exprs[,chan]
  x.norm <- normalisation[[chan]](x)
  plot(density(logicleTransform()(x)))
  lines(density(logicleTransform()(x.norm)),col='red')
  lines(density(logicleTransform()(beads1@exprs[,chan])),col='green')

Ok so these curves don't align well. Why? This is the regression on log10 scale:

plot(log10(MFI.beads1[,chan])  ~ log10(MFI.beads2[,chan]))
abline(lm(log10(MFI.beads1[, chan]) ~ log10(MFI.beads2[, chan])))

This is the regression on linear scale:

plot((MFI.beads1[,chan])  ~ (MFI.beads2[,chan]))
abline(lm((MFI.beads1[, chan]) ~ (MFI.beads2[, chan])))

  my.log10 <- function(x) ifelse(x<=0,0,log10(x))
  chan <- 'APC-AF750-A'
  x <- beads2@exprs[,chan]
  x.norm <- normalisation[[chan]](x)
  plot(density(my.log10(x)))
  lines(density(my.log10(x.norm)),col='red')
  lines(density(my.log10(beads1@exprs[,chan])),col='green')

(to be continued...)