Pregated in FlowJo before PeacoCO and how to solve error "valid transformList" in flowCore::transform to transform spectral data?

[denvercal1234GitHub]

Hi there,

Thank you for the package.

QUESTION 1. I have some spectral flow data. My population of interest for analysis if live T cells. To use PeacoQC, should I first gate on the population of interest and remove doublets and use Time gate etc in FlowJo first? Or should I simply used the whole unprocessed (but unmixed) FCS files of all events acquired?

QUESTION 2. To transform the spectral data before doing PeacoQC(), what should I set for the $SPILL keyword because if I run ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff, colnames(flowCore::keyword(ff)$SPILL))), I encountered an error below.

Thank you again for your help.

> ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff, colnames(flowCore::keyword(ff)$SPILL)))
Error in .local(`_data`, ...) : 
  'from' and 'to' must be character vectors of equal length. !Please make sure the unnamed argument is a valid 'transformList' object!