Check out this work flow for R based flow cytometry

https://www.bioconductor.org/help/workflows/highthroughputassays/flowWorkFlow.pdf

You should check out flowCore it provides functionality to coerce an FCS file input to a matrix format. Be aware in the process you will lose the metadata associated with the experiment run, like experiment name etc.

I have used the exprs function in flowCore to convert to a matrix form. If you go to the link attached check out exercise 2 on page 2.

I am currently working on a PhD on the Automated Gating of Cytometry data from a statistics viewpoint so any other questions I am happy to help out :)

https://www.bioconductor.org/help/course-materials/2007/BioC2007/labs/flowcore1/flowBasics-solved.pdf

Thank you for your help. I believe Kevin you're missing the link you talk about in the comment for Ex#2? And, yes, that is great! I'll definitely be asking more questions soon. do you use openCyto for automated gating or do you just use different algorithms and work on single .FCS file? (In my case, i'm working with 81 patients/3 .FCS files per patient) and thus, i'm creating an automated analysis pipeline to analyze this data as a batch.

Apologies for the missing link forgot to click the Add button, attached above now. 

So from a statistics viewpoint flowClust (Part of OpenCyto) is the leading automated gating solution. I don't work with OpenCyto directly but rather developing my own gating techniques in R. My work mainly focuses on a single .FCS file but simply because the adaption of my methods to batches would be fairly simple once I have it up and running for single files.

Very interested to see how you go about the automated pipeline for analysing your data, as a statistician its nice to see what the biologists actual want rather then me trying to guess.

yes, I believe flowClust at least to me, provides that non-supervised gating in identifying overlapping populations in gaussian distribution. Then are you using existing algorithms to incorporate them into some pipeline?

I have incorporated several gating functions outside of openCyto into it, to use them in creating a gating template.

If you're interested, i use all the information in the .fcs files (such as SPILL & channel names) to compensate the raw data, I filter before that using flowClean (but would appreciate in case if you can suggest other cleaning methods, since flowClean takes some time & uses the time interval difference between cells). Then I transform and create a gating set out of those .FCS files. Since our gating scheme involves around 23 2-dimensional gatings, i have created a gating template in the form of .csv file as they suggest in openCyto & i'm currently gating applying all this to my data.

i've also tried SPADE & FlowSOM on my data & they give a different perspective for analysis. if you need more detailed info with all the packages & explanations, let me know

Try to contact directly OpenCyto guys, Greg Finak or Mike Jiang. They are always open to support OpenCyto users. Try here https://support.bioconductor.org/t/opencyto/.

Cheers!