I have 23 samples of scRNA-seq data with similar cell types. When I run cellphonedb without subsampling, for some samples the results (e.g., singificant_means, means) do not have all cell-cell interactions (columns). Does it mean that cellphonedb couldn't find any interactions between those cell pairs? So, those cell types do not interact at all?
Also, for rank calculation, you wrote
"The rank is calculated by counting the significant p-values per interaction pair (per row) and dividing with the total number of cluster-cluster comparisons."
Does that formula include all cluster-cluster comparisons (potentially interacting cells) or only those included in the final results?
thank you
I have 23 samples of scRNA-seq data with similar cell types. When I run cellphonedb without subsampling, for some samples the results (e.g., singificant_means, means) do not have all cell-cell interactions (columns). Does it mean that cellphonedb couldn't find any interactions between those cell pairs? So, those cell types do not interact at all?
Also, for rank calculation, you wrote
Does that formula include all cluster-cluster comparisons (potentially interacting cells) or only those included in the final results? thank you