-
Notifications
You must be signed in to change notification settings - Fork 142
error when calling identifyOverExpressedGenes function #186
Comments
@idupanloup For the merged cellchat object, you cannot run |
@sqjin I ran CellChat on the 2 datasets and now get a new error message: db1data.input <- GetAssayData(db1.Seurat, assay = "RNA", slot = "data") # normalized data matrix db1.cellchat@DB <- CellChatDB.use db1.cellchat <- subsetData(db1.cellchat) db1.cellchat <- computeCommunProb(db1.cellchat, raw.use = TRUE) Filter out the cell-cell communication if there are only few number of cells in certain cell groupsdb1.cellchat <- filterCommunication(db1.cellchat, min.cells = 10) db1.cellchat <- computeCommunProbPathway(db1.cellchat) Compute the network centrality scoresdb1.cellchat <- netAnalysis_computeCentrality(db1.cellchat, slot.name = "netP") db2data.input <- GetAssayData(db2.Seurat, assay = "RNA", slot = "data") # normalized data matrix db2.cellchat@DB <- CellChatDB.use db2.cellchat <- subsetData(db2.cellchat) db2.cellchat <- computeCommunProb(db2.cellchat, raw.use = TRUE) Filter out the cell-cell communication if there are only few number of cells in certain cell groupsdb2.cellchat <- filterCommunication(db2.cellchat, min.cells = 10) db2.cellchat <- computeCommunProbPathway(db2.cellchat) Compute the network centrality scoresdb2.cellchat <- netAnalysis_computeCentrality(db2.cellchat, slot.name = "netP") merged.cellchatobject.list <- list(db1 = db1.cellchat, db2 = db2.cellchat) Merge the following slots: 'data.signaling','net', 'netP','meta', 'idents', 'var.features' , 'DB', and 'LR'.merged.cellchat@DB <- CellChatDB.use gg1 <- compareInteractions(merged.cellchat, show.legend = F, group = c(1,2)) netVisual_diffInteraction(merged.cellchat, weight.scale = T) Error in obj2 - obj1 : non-conformable arraysDo you know what can be the problem ? |
@idupanloup Sorry. I missed your information. I guess the reason is that you have different cell groups between the two datasets. If so , please check the third tutorial. |
I get an error when calling the identifyOverExpressedGenes function.
Here's my code:
Many thanks for your feedback !
The text was updated successfully, but these errors were encountered: