Hi - what can be done if cell_signaling() does not find any interaction between clusters?
> ND_clusters_copy$numbers[1] 998 294 355 821 1081 935 781 933 10 824 1649 303 443 307 1900 1 1
There should be enough cells in each cluster to find a difference (apart from the last two, which I added manually). Also, it does not find all 17 clusters, only the first 15, although it does look for DGE:
...No such file as table_dge_cluster 17.txt in the cluster-analysis folder...
I guess not finding the dge table is normal as it happend also in the vignette on bioconductor.
But:
...0 No significant interaction found from cluster 1 to cluster 150 No significant interaction found from cluster 2 to cluster 1...
A bit more info:
>ND_signal <- cell_signaling(data = ND_merged, genes = rownames(ND_merged), cluster = ND_clusters_copy$cluster, write = FALSE)> nrow(ND_merged)[1] 21532> length(ND_clusters_copy$cluster)[1] 11636
Hi - what can be done if cell_signaling() does not find any interaction between clusters?
> ND_clusters_copy$numbers[1] 998 294 355 821 1081 935 781 933 10 824 1649 303 443 307 1900 1 1There should be enough cells in each cluster to find a difference (apart from the last two, which I added manually). Also, it does not find all 17 clusters, only the first 15, although it does look for DGE:...No such file as table_dge_cluster 17.txt in the cluster-analysis folder...I guess not finding the dge table is normal as it happend also in the vignette on bioconductor. But:...0 No significant interaction found from cluster 1 to cluster 150 No significant interaction found from cluster 2 to cluster 1...A bit more info:>ND_signal <- cell_signaling(data = ND_merged, genes = rownames(ND_merged), cluster = ND_clusters_copy$cluster, write = FALSE)> nrow(ND_merged)[1] 21532> length(ND_clusters_copy$cluster)[1] 11636Thanks for helping!