Entering edit mode
10 months ago
Aydin
•
0
Hi, I'm having an error similar to this cellchat user (https://github.com/sqjin/CellChat/issues/264). If I run CellChatDB.mouse, and I subset my cellchat object (subsetData), I get this error:
Error in identifyOverExpressedGenes(cellchat_DMSO) :
Please check `object@data.signaling` and ensure that you have run `subsetData` and that the data matrix `object@data.signaling` looks OK
When I look at the data.signalling matrix of my cellchat object, I see 2 rows:
> cellchat_DMSO@data.signaling
2 x 10547 sparse Matrix of class "dgCMatrix"
[[ suppressing 66 column names ‘AAACCCAAGAATTCAG-1’, ‘AAACCCACAACCCTCT-1’, ‘AAACCCACACCAGCCA-1’ ... ]]
C3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.183826 . . . . . .
F2 . . . . . . . . . 2.642966 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C3 . . ......
F2 . 0.943755 ......
.....suppressing 10481 columns in show(); maybe adjust 'options(max.print= *, width = *)'
..............................
I do not get this same error when I use CellChatDB.human. How can I fix my data.signalling matrix? For reference, my cellchat object came from Seurat input.
Thank you for your help!
