GetFlowJoLabels

[Aminach1]

Hello,

Thank you for the great package!

I wanted to extract the manual labels with the function "GetFlowJoLabels" so that I can establish a comparison between manual and automated. Unfortunately, I got the error message: Error in manualMatrix[, cellType] : subscript out of bounds

gatingResult <- GetFlowJoLabels(fcs.dir, wspFile,
cellTypes = cellTypes,
getData = TRUE, sample_names_from="sampleNode")

Do you have any ideas how I could solve this?
Thank you!

[gmillerscripps]

Hi @Aminach1 are you confident that all of your cellTypes are present in the flowJo workspace?

You could start with:

gatingResult <- GetFlowJoLabels(fcs.dir, wspFile,
cellTypes = NULL,
getData = TRUE, sample_names_from="sampleNode")

and then look at: print(levels(gatingResult[["manual"]])) to determine if your cellTypes are present.

Hope this helps. If this works, I am curious to know if the results match the gated numbers that you see in your flowJo workspace.