error in annotation and Isotype argument

[yaozhan2022]

Hi,

I was running the infinity flow pipeline, but keeps getting error messages. Wondering could you please give some advise? Thank you!

imputed_data <- infinity_flow( path_to_fcs = '/path/to/fcs/files', #input_dir, path_to_output = path_to_output, path_to_intermediary_results = path_to_intermediary_results, backbone_selection_file = backbone_specification, annotation = targets, isotype = isotypes, input_events_downsampling = 2000,#input_events_downsampling, prediction_events_downsampling = 500,#prediction_events_downsampling, verbose = TRUE, cores = cores )

The following values from the isotype argument are not matching any of the values from the annotation argument: NA, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG1, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k, mouse IgG2a, k,

File.annotation_ENG-001.csv

[yaozhan2022]

fixed. thanks

[Sandyna]

But... How? I have the same problem

Edit: I solved mine too, you need to have fcs files for each isotype control and they need to have the target and isotype named identically in the annotation