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saeyslab / CytoNorm

R library to normalize cytometry data
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Error in the step of training the model #41

Open ctjimmyhsu opened 1 year ago

ctjimmyhsu commented 1 year ago

Using the data from the flow repository, I succesfully ran the code and steps until receiving an error at the training model step. The error was "Error in FlowSOM::AggregateFlowFrames(files, nCells, channels = colsToUse, : unused argument (channels = colsToUse)"

I doubled check all the previous steps, and the data structure and input seem to be fine. Are there any suggestions?

m-nikolaidis commented 6 months ago

Based on the documentation there is no parameter channels. This might be giving you the error

SamGG commented 6 months ago

Based on the documentation of the current FlowSOM package, there is a channels argument. https://bioconductor.org/packages/release/bioc/manuals/FlowSOM/man/FlowSOM.pdf page 12 @ctjimmyhsu The version you are using is probably not the latest one. @m-nikolaidis Thanks for pointing the discrepancy.