NAs are not allowed in subscripted assignments

[HelgaBergholtz]

I have data from just a few markers from a Vectra Polaris experiment (see attached files). When I try to run AssignCells(), I get this error message:

Error in current_scoring_matrix[unassigned_cells, cell_type_num[i]] <- GetScore(activation_prob_to_use, : NAs are not allowed in subscripted assignments

I have tried both with and without prior filtering and the same happens.
Can you help me understand what I am doing wrong?
imaging_data_test.txt
marker_info_test.txt

[weiruo16]

I have data from just a few markers from a Vectra Polaris experiment (see attached files). When I try to run AssignCells(), I get this error message:

Error in current_scoring_matrix[unassigned_cells, cell_type_num[i]] <- GetScore(activation_prob_to_use, : NAs are not allowed in subscripted assignments

I have tried both with and without prior filtering and the same happens. Can you help me understand what I am doing wrong? imaging_data_test.txt marker_info_test.txt

My intuitive guess is that there is a conflict of marker information in your cell type signature matrix. The CD4 T cells were identified requiring low expressions of CD8, but in the second round, the CD4 T cells were used to identify a subset of CD8 high cells. I made a slight change to correct that in the your "marker_info_test.txt" file, and it ran without errors using the default settings.
marker_info_test_Modified.txt