jinworks
error when running IdentifyOverExrpessedGenes
at the moment to run IdentifyOverexpressedGenes() i get:
Error in identifyOverExpressedGenes():
! Please check [email protected] and ensure that you have run subsetData and that the data matrix [email protected] looks OK.
script: data.cc <- GetAssayData(Data_set), assay = "SCT", layer = "data") #Data_set[["SCT"]]$data labels <- Idents(Data_set) meta <- data.frame(samples = labels, row.names = names(labels)) # create a dataframe of the cell labels
cellchat <- createCellChat(object = Data_set, group.by = "samples")
CellChatDB <- CellChatDB.human # use CellChatDB.mouse if running on mouse data showDatabaseCategory(CellChatDB) dplyr::glimpse(CellChatDB$interaction)
use a subset of CellChatDB for cell-cell communication analysis
#CellChatDB.use <- subsetDB(CellChatDB, search = "Secreted Signaling", key = "annotation") # use Secreted Signaling
Only uses the Secreted Signaling from CellChatDB v1
CellChatDB.use <- subsetDB(CellChatDB, search = list(c("Secreted Signaling"), c("CellChatDB v1")), key = c("annotation", "version"))
use all CellChatDB except for "Non-protein Signaling" for cell-cell communication analysis
CellChatDB.use <- subsetDB(CellChatDB)
use all CellChatDB for cell-cell communication analysis
CellChatDB.use <- CellChatDB # simply use the default CellChatDB. We do not suggest to use it in this way because CellChatDB v2 includes "Non-protein Signaling" (i.e., metabolic and synaptic signaling).
set the used database in the object
cellchat@DB <- CellChatDB.use
subset the expression data of signaling genes for saving computation cost
cellchat <- subsetData(cellchat) # This step is necessary even if using the whole database future::plan("multisession", workers = 4) # do parallel cellchat <- identifyOverExpressedGenes(cellchat)
@bontix-77 Have you fixed the issue?
yes, but it fixed by itself. I don't know what was the root problem., at some point it simply start working....... mystery!