Hi all,

I'm using flowPeaks in combination with flowCore and flowViz to identify clusters in flow cytometry data.  I can get adequate clustering of my flow frame, and now I want to get summary statistics for each identified cluster (median fluorescence intensity for each parameter etc.).  I can't find any way of subsetting my flow frame to only include particular clusters to get this summary information.  Am I able to do this?  Any help would be much appreciated.  This is the code I used to get my clusters:

> library(flowCore)
> library(flowPeaks)
> library(flowViz)
> data <- read.FCS("C:\\Users\\Hefin\\Documents\\Stats\\Sepsis Patient 11 BC 01102012_B AV+41.fcs")
> summary(data)
> lgcl <- estimateLogicle(data, channels = c("FSC-A", "SSC-A", "B530/30-A", "V450/50-A"))            #derive logicle transformation function
> transformed <- transform(data, lgcl)   #apply transformation function to flow frame
> summary(transformed)
> plot(transformed[,c(1,2,3,6)], smooth = F)
> cluster <- flowPeaks(transformed@exprs[, c(1,2,3,6)], t = 0.4, h0 = 0.255, h = 0.255)     #cluster based on
> par(mfrow = c(2,3))
> plot(cluster, idx = c(1,2,3,4), drawkmeans = F)
> assigned <- assign.flowPeaks(cluster, cluster$x, tol = 0, fc = 0)                #get cluster labels
> plot(cluster, idx = c(1,2,3,4), classlab = assigned, drawlab = T, drawkmeans = F)

Thank you in advance!

Hefin Jones, MPharmacol
PhD Student
Biochemical Pharmacology
William Harvey Research Institute
John Vane Science Centre
Charterhouse Square
London EC1M 6BQ

h.r.jones@qmul.ac.uk
+4420 7882 5652


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