Table of Contents Standalone Application (MATLAB not required) Software Prerequisites Installing the Normalizer Running the Normalizer in MATLAB

The bead-based Normalizer for mass cytometry data is distributed as a standalone MATLAB application. That means that it requires installing the MATLAB Compiler Runtime (MCR), but an installation or license for MATLAB itself is not required. It is important to install corresponding releases of the MCR and the Normalizer; v0.2 of the Normalizer requires

• MCR Release R2013b (8.2) for Mac OSX
• MCR Release R2013a (8.1) for 64-bit Windows

Instructions for download and installation of the MCR are available here.

The Normalizer is available here: https://github.com/nolanlab/bead-normalization/releases

Simply download and unzip the version corresponding to your operating system.

You are now ready to normalize FCS files.

Download the source code, and also download the FCS reader and writer available in the MatlabCytofUtilities repository. To run the Normalizer, at the prompt type

>> normalize_folder(optional_bead_removal)

where

optional_bead_removal = true

if you want to include the bead removal step, and

optional_bead_removal = false

to skip the bead removal step.

You are now ready to normalize FCS files.