Playing with flow cytometry data in R....

So, I have been using Amy's flow data to try and grapple with data into R.

Making some progress!

I have managed to get some FCS data into R:

ntl<-read.FCS("A01 NTL.fcs")

plot(ntl, c("FSC-A", "SSC-A"), xlim=c(0, 5000000), ylim=c(0, 500000))

draws a nice dot plot:

So there is a data format issue. We have:

• Formal class flowSet
• Large flowFrame
• Formal class workFlow

According to this: http://master.bioconductor.org/help/course-materials/2010/BioC2010/intro.pdf

flowFrame - a class representing the data contained in a FCS file.

1. raw measurement

2. keywords in the FCS files

3. annotation for parameters (stains, sample names, range)

flowSet - a collection of flowFrame.

So it is possible to do gating but I am finding it difficult to understand and make work. 

Some info here but it's a bit challenging:

http://master.bioconductor.org/help/course-materials/2010/BioC2010/AnalyzingFlowData.pdf