What do "PnBS" and "PnMS" mean in FCS flowCore parameters?

Question

I'm using the flowCore packages to analyze cytometry data, and I am trying to understand all the parameters stored in the FCS file. I've figured out most of the elements, but despite a thorough search I haven't been able to find documentation on some of the parameters.

For each channel, there are 9 associated parameters. Here's P1 and its associated values from one of my files :

• $P1N FSC-A
• $P1R 262144
• $P1B 32
• $P1E 0,0
• $P1V 225
• $P1G 1
• $P1DISPLAY LIN
• $P1BS 0
• $P1MS 0

I've figured out the following from various sources (notably the FCS data standards, given here) or from the fields themselves:

• $PnN Short name for parameter n.
• $PnR Range for parameter number n.
• $PnB Number of bits reserved for parameter number n.
• $PnE Amplification type for parameter n.
• $PnV Detector voltage for parameter n.
• $PnG Amplifier gain used for acquisition of parameter n.
• $PnDISPLAY the transformation to apply when displaying the data (e.g. LIN, LOG)

However, these 2 don't appear in the file standard description, and flowCore does not have documentation on the parameters either.

• $PnBS
• $PnMS

I've seen $PnBS set at -1, 0, 48, 57, 54, 52 or 25 for various channels in my data, while $PnMS always seems to be at 0.

Does someone know what it is, or where to look for a definition? If that helps, my FCS files were generated through BD FACSDiva Software Version 9.0.1.

Answer 1

I found my answer in an old mailing list. Credit to Josef Spidlen who authored the mail.

Short answer: both parameters are proprietary keywords from the BD FACSDiva software for storing scaling values.

Long answer from the mailing list:

PnBS Indicates the automatically set Biexponential scale value for Instrument Parameter (-1 indicates an invalid scale value). When importing an FCS file, if the FCS file has valid Biexponential scales, they should be applied to the data. If the FCS file doesn't have valid biexponential scales then the scales are calculated from the entire data. If biexponential scales exist, then if AUTOBS is set, the PnBS values are used and applied to the data. If AUTOBS is not set, the PnMS values are used and applied to the data. The information represented by this keyword becomes part of a Tube's attributes, and does not appear in the Tube's list of keywords. It can be viewed in the Biexponential inspector' when the auto scaling option is selected.

PnMS Indicates the manually set Biexponential scale value for Instrument Parameter (-1 indicates an invalid scale value). When importing an FCS file, if the FCS file has valid Biexponential scales, they should be applied to the data. If the FCS file doesn't have valid biexponential scales then the scales are calculated from the entire data. If biexponential scales exist, then if AUTOBS is set, the PnBS values are used and applied to the data. If AUTOBS is not set, the PnMS values are used and applied to the data. The information represented by this keyword becomes part of a Tube's attributes, and does not appear in the Tube's list of keywords. It can be viewed in the Biexponential inspector' when the manual scaling option is selected.