Open Tomer9w opened 3 years ago
@Tomer9w You should use the normalized data (i.e. log-transformed data) instead of the raw count data
I switched to the normalized data, but still same error message.
A snip from the relevant input table:
Thanks
Hi, I meet the same problem. This error have occur in my a small portion of the sample. And it run successful in other with the same code. How can I find more detail error message to fix the error.
@chen-zhan The best way is to run the source codes and see when this error happens.
Hi! Thanks for this awesome package I've seen this question asked before, but unfortunately, neither of recommendations helped me overcome this error.
I used RNA-seq normalzied counts as input for cellchat object. Here is the code I used:
`cellchat <- createCellChat(object = as.matrix(input.DLN), meta = coldata, group.by = "Type") cellchat <- setIdent(cellchat, ident.use = "Type") groupSize <- as.numeric(table(cellchat@idents)) CellChatDB <- CellChatDB.mouse # use CellChatDB.mouse if running on mouse data showDatabaseCategory(CellChatDB)
cellchat@DB <- CellChatDB cellchat <- subsetData(cellchat) # This step is necessary even if using the whole database future::plan("multisession", workers = 4) # do parallel
cellchat <- identifyOverExpressedGenes(cellchat) cellchat <- identifyOverExpressedInteractions(cellchat) cellchat <- projectData(cellchat, PPI.mouse)
cellchat <- computeCommunProb(cellchat, raw.use = TRUE) cellchat <- filterCommunication(cellchat, min.cells = 10) `
Here is a snip of the input.DLN data frame
Hope you can help with this Thanks!