WHY: spectral instruments (e.g. Sony ID7000) write already-unmixed data and carry no $SPILLOVER keyword. Compensating twice, or erroring because the matrix is absent, are both wrong – detect and report.
Arguments
- ff_exprs
The ff exprs.
- keywords
FCS keyword list.
- external
A spillover matrix from
read_spillover_file(), or NULL.
Value
ff_exprs, compensated where a matrix applied, with attribute
compensation stating what was done.
Details
WHAT AN ABSENT KEYWORD MEANS. Nothing, on its own. $SPILLOVER is the only
standard carrier of a compensation matrix (FCS 3.1, Spidlen et al. 2010), so
a file without it is either unmixed or compensated already, or conventional
data nobody compensated. The keyword cannot tell those apart, and the result
says the status is unknown rather than guessing the reassuring answer. FCS 3.2
files can say it per parameter in $PnTYPE ("Unmixed_Fluorescence"), and
that is read where it is written.
A MATRIX FROM ELSEWHERE. external, from --spillover, replaces the file's
own matrix: a matrix recomputed from single-stain controls, in AutoSpill or in
the acquisition software, is applied to every file instead of whatever the
files carry.