Open sierranishizaki opened 4 months ago
Hi sierranishizaki,
Another (though less likely) reason for AllCountsFilteredException may be that your genes do not overlap with those in CellphoneDB database: https://github.com/ventolab/cellphonedb-data/blob/master/data/gene_input.csv Could you please confirm whether or not any of the genes in adata.var occur in the above file?
Best,
Robert.
Thanks for the speedy response Robert! It appears that 208 of the 2k genes in my dataset have a match in gene_input.csv.
Just checking, is adata.var the place in the AnnData file CellPhoneDB is looking for gene names?
Hi sierranishizaki,
CellphoneDB is looking for gene names in the index of adata.to_df().T - hope that helps.
Best,
Robert.
Is there a reason y'all can think of that I would be getting an 'all counts filtered' error when using human genes?
I started with a mouse Seurat object and converted into a h5ad object with human genes using the orthogene package. When running my whole ~42k cell dataset I got "No Interactions Found". I saw in another post that that error may be caused by too many cells, so now I've subset my data to 28k cells and am getting this error message:
Double checking, my gene names do appear to be human (filtered for only 1-to-1 genes).
Any hints as to why I can't seem to get this data to behave in CellPhoneDB would be appreciated!