Normalizer v0.3

This release (v0.3) of the Normalizer contains the following updates:

• The 'Event_length' channel in CyTOF2 data is no longer being normalized. Previously the Normalizer was excluding the 'Cell_length' channel in CyTOF1 data but not the equivalent channel with the updated 'Event_length' label in the CyTOF2.
• The bead singlet events identified before normalization, and the events removed after normalization, are saved in separate folders.
• The bug that prevented users from being able to select previously created files of beads to use as a normalization baseline has been fixed.
• The source code now includes p-code for several helper functions that were previously omitted.
• Closing the figure window gives the user an option to quit mid-normalization.
• The FCS reader and writer needed to run the Normalizer using the source code within Matlab are now available in the MatlabCytofUtilities repository. Make sure to use the versions there since they have several updates and fixes as compared to other versions. (They are still automatically included in the standalone application so no need to download them if you are using the MCR.)

For instructions about installing and running the Normalizer, see the wiki.

To learn more about normalization of mass cytometry data or to cite the Normalizer, see the article in Cytometry.

Normalizer v0.2

This release (v0.2) of the Normalizer contains the following new features:

• The bead mass selection step is now initially listed as three options: the beads available from DVS/Fluidigm, the beads which with the method was developed, and the option to choose any set of custom masses. The commercially available beads are the default.
• Large files are sampled for visualization in both the bead gating and bead removal steps. The boundaries or cutoffs chosen are then applied to all events in the file.
• FCS files created from both the CyTOF and the CyTOF2 are supported.
• In addition to the FCS file of normalized removed events that is created for each input FCS file, an FCS file of the unnormalized gated beads is also saved.
• In addition to the option to normalize to the median level of the set of input files (the previous default), there is now also the option to normalize to previously gated beads. This would allow one normalize additional files to a set of previously normalized files, or to choose a particular baseline such as from the start of an experiment. The unnormalized beads files that are now being saved are compatible input for this baseline normalization.

and the following bug fixes:

• The bug that resulted in improper before/after visualization when normalizing only one FCS file has been fixed.

Update 2014-10-21:

• The 'Event_length' channel in CyTOF2 data is no longer being normalized. Previously the Normalizer was excluding the 'Cell_length' channel in CyTOF1 data but not the equivalent channel with the updated 'Event_length' label in the CyTOF2.

For more information, see the wiki and/or the article in Cytometry.