estimates scale tranformations

this function estimates the scale transformations to be applied on a flowFrame to obtain 'good behaving' distributions, i.e. the best possible separation between + population and - population. It distinguishes between scatter channels, where either linear, or no transform is applied, and fluo channels, where either logicle transform

• using flowCore::estimateLogicle - is estimated, or no transform is applied.

The idea of linear transform of scatter channels is as follows: a reference channel (not a scatter one) is selected and a linear transform (Y = AX + B) is applied to all scatter channel, as to align their 5 and 95 percentiles to those of the reference channel For the estimateLogicle function, see flowCore documentation.

estimateScaleTransforms(
  ff,
  fluoMethod = c("estimateLogicle", "none"),
  scatterMethod = c("none", "linearQuantile"),
  scatterRefMarker = NULL,
  specificScatterChannels = NULL,
  verbose = FALSE
)

Arguments

ff

a flowCore::flowFrame

fluoMethod

method to be applied to all fluo channels

scatterMethod

method to be applied to all scatter channels

scatterRefMarker

the reference channel that is used to align the

specificScatterChannels

vector of scatter channels for which we still want to apply the fluo method (and not the scatter Method)

verbose

if TRUE, send messages to the user at each step

Value

a flowCore::flowFrame with removed low quality events from the input

Examples

data(OMIP021Samples)

compMatrix <- flowCore::spillover(OMIP021Samples[[1]])$SPILL
ff_c <- runCompensation(OMIP021Samples[[1]], spillover = compMatrix)

transList <- 
    estimateScaleTransforms(        
        ff = ff_c,
        fluoMethod = "estimateLogicle",
        scatterMethod = "linear",
        scatterRefMarker = "BV785 - CD3")