WHAT: an event is at the margin when, in any of the channels used, it is at
or above that channel's highest value (margin_at from
linearise_channels()).
Arguments
- ex
Expression matrix, linear units.
- scale
The
scaletable fromlinearise_channels().- used
Column indices judged: the marker and scatter channels.
- warn_frac
Warn when more than this fraction of events is at a margin. Default
0.01.- label
File name for the log line.
Value
list(event = logical per event, n = count, by_channel = named integer count per judged channel with any)
Details
WHY THEY ARE REMOVED RATHER THAN KEPT. A saturated event has no true value in
the saturated channel: it is somewhere above the top, by an unknown amount.
flowAI removes "margin events in the upper limit of the dynamic range"
(Monaco et al. 2016) and PeacoQC's RemoveMargins() does the same (Emmaneel
et al. 2022). Capping them instead, which flowCore's read.FCS() and earlier
versions of this package did, keeps the event and invents a value for it: a
pile of identical values at the top of the scale. Floating-point files can
also carry values far above the declared range, up to 6.8e8 under a declared
262,144 on one cohort, which are not measurements at all.
On the 30 spectral files of one sepsis cohort the margin events were 0.01% to 0.7% of each file. A file losing more than 1% is named in a warning, because at that rate the voltage was set too high or the declared range is wrong.