Open cathalgking opened 1 year ago
I seem to have got this working with the following code, but am getting an error for one of my Seurat objects.
D1_scMAGIC <- scMAGIC_atlas(exp_sc_mat = D1_seu@assays$SCT, MCA_ref, atlas = 'MCA')
Error in checkForRemoteErrors(val) : 4 nodes produced errors; first error: probabilities must be finite, non-negative and not all 0
Do you know why this might be? I have almost the same type of object but with different data and have not gotten that error.
Any help would be greatly appreciated.
A count matrix should be input to "exp_sc_mat ". So, you can try to use the following code:
D1_scMAGIC <- scMAGIC_atlas(exp_sc_mat = D1_seu@assays$RNA@counts, MCA_ref, atlas = 'MCA', type_ref = 'sum-counts', use_RUVseq = F)
I have a Seurat object and I would like to do a 'Reference-free annotation' with scMAGIC. How can I do this? I have tried various options with the data and have had no luck.