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This repository has been archived by the owner on Jan 24, 2024. It is now read-only.
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
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.
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!
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