Hi Adeeb,
I haven't used Fluidigm's algorithm so far, just the MATLAB one.
However, there are definitely some differences between the methods. Fluidigm has a document talking about some of this:
https://www.fluidigm.com/documents (CyTOF, "Normalization of Mass Cytometry Data using EQ Four Element Beads")
From that:
"Two algorithmic processing options are available for normalization of data collected in .fcs file format. Both methods normalize for intra- and inter-file signal drift.
1. Fluidigm (DVS) method: Available on CyTOF SW version 6.0.626 and above. This method normalizes data to a global standard determined for each lot of manufactured EQ Beads, and allows normalization of data within and across experiments as well as across instruments The information for each lot of EQ Beads
is captured in the form of a “Passport”. The software is pre-loaded with passports for all the manufactured bead lots. See Appendix A for a complete description of this normalization method. Note: Eu Beads do not have Passport values assigned and data collected using these
beads must be normalized using the MATLAB Method, described below.
2. MATLAB® Method: Available through freeware offered by Stanford University. This method normalizes data using median bead intensity calculated from across the experimental data files instead of a global predetermined standard (Finck et al, Cytometry A 83:483)."
So, one major difference is that Fluidigm/PASSPORT normalizes everything to effectively an external value, the "global standard determined for each lot of manufactured EQ Beads". In contrast, the MATLAB/Finck et al method uses "median bead intensity calculated from across the experimental data files instead of a global predetermined standard".
It's my opinion that the MATLAB method should do a better job of capturing how the machine is performing on that particular day, in that particular sample. But I have not rigorously tested this, and I would love to hear other opinions/comments.
Mike