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plevritis-lab / CELESTA

Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information for multiplexed in situ imaging data. No training dataset with cell type labels is required.
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NAs are not allowed in subscripted assignments #22

Open HelgaBergholtz opened 8 months ago

HelgaBergholtz commented 8 months ago

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 commented 8 months ago

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 plot_cell_assignment