Gordon Beattie
Gordon Beattie
Thanks for the suggestion, I've tried that, and I've tried setting `trim = 0` just to check whether that helps, neither resulted in any more interactions coming through. To double...
Did you find a solution in the end? I am having the same issue!
> This code is for exacting cell embeddings such as tsne or umap, you have to `RunTSNE` to get this slot. > > Also make sure you are using Seuratv2...
Thanks for the response, I can confirm the cell_ID has some non-zero values, although most of them are 0. I'll put a few metrics below to give a little more...
@sqjin I'm afraid not, I'm currently relying on generating a fold change comparison between communication probabilities in each condition to find differences, which likely isn't ideal.
@tomthomas3000 Just to confirm yes I do find the same interactions in net.up and net.down. I've tried playing with subsetCommunication and can't quite see any pattern as to why it's...
@tomthomas3000 Both the interactions and the genes themselves overlap unsurprisingly, see below for my working. I wouldn't be as concerned over a little overlap between the genes, since individual genes...