SofieVG/FlowSOM

unable to find an inherited method for function ‘compensate’ for signature ‘"flowFrame", "NULL"’

yueli8 opened this issue · 2 comments

Hello,

Thank you for developing so nice software.

It goes well with the demo data of "68983.fcs", but gets wrong with my data.

Thank you in advance for your great help!

Best,

Yue

fileName <- system.file("extdata", "s_Processed.fcs", package="FlowSOM")
ff <- flowCore::read.FCS(fileName)
comp <- flowCore::keyword(ff)[["SPILL"]]
ff <- flowWorkspace::compensate(ff, comp)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘compensate’ for signature ‘"flowFrame", "NULL"

s_Processed.zip

SamGG commented

This is not a FlowSOM error. The compensate function of the flowWorkspace package requires a gating strategy or cytoFrame or cytoSet whereas the compensate function of the flowCore package uses a flowFreame. This might be misleading, but as you prefix the function by the package name, I assume that you know what you are doing. Interpreting such an error is not straightforward at first sight, but always try understand the error on your own or with the help of people around you. Learning R is not easy, but you will get benefits. Cheers.