RGLab/flowCore — pull request #14 by jspidlen (2013-11-14 19:01:06+00:00)
Title: FCS PnG based scaling support

I added a new option to read.FCS(..., transformation="linearize-with-PnG-scaling"). This does "linearization" for log-stored parameters and also division by gain (value of the $PnG keyword) for linearly stored parameters. This is how the channel-to-scale transformation should be done according to the FCS specification (and according to Gating-ML 2.0), but lots of software tools are ignoring the $PnG division (since it is just a linear transformation and not critical in many cases). Therefore, I added it so that it is only done when specifically asked for so that the read.FCS method remains backwards compatible with previous versions. Also, when an FCS file is read with the transformation="linearize-with-PnG-scaling" then I am adding a flowCore_fcsPnGtransform keyword in the flowFrame@description set to "linearize-with-PnG-scaling".