Flow cytometry analysis using Bioconductor

Question

[Nitin]

Hello,

I have set of raw .fcs files from flow cytometer, I am new to computational analyses of FCS data can anybody clarify following basic doudt

Should I first perform quality control of FCS file and followed by transformation? or other way round first transformation and quality control of raw FCS data?

Thanks, Sai

Answer 1

[ddiez]

I am assuming you have taken a look at the flow cytometry list of packages in Bioconductor. What package/s are you using? In the packages documentation there should be some information about basic analyses. Also take a look at the workflows, in particular this one, that links a PDF describing a typical flow cytometry workflow. In particular, there is a sentence saying:

We begin by reading in flow cytometry data from raw FCS files, storing them in appropriate data structures and performing quality control checks on the data.

Quickly reading the PDF workflow suggests you first do transformation then quality control. But I have no direct experience with these packages, so you should probably read this document in detail.