identifyOverExpressedGenes errors:subscript out of bounds

[songeric1107]

same problem as reported before, still no solution.

iso <- subset(x =frc.sub, subset = orig.ident == "naive")

iso.data.input = as.data.frame(GetAssayData(iso,assay = "RNA",slot = "data")) # normalized data matrix

#iso.data.input.f=iso.data.input[which(rowSums(iso.data.input)>0),]

iso.meta=[email protected]

cellchat.iso <- createCellChat(object = as.matrix(iso.data.input.f), meta = iso.meta, group.by = "rename_cluster_222")
cellchat.iso <- setIdent(cellchat.iso, ident.use = "rename_cluster-222") # set "labels" as default cell identity
levels(cellchat.iso@idents) # show factor levels of the cell labels
groupSize <- as.numeric(table(cellchat.iso@idents))

Issue identified!! Please check the official Gene Symbol of the following genes: H2-BI H2-Ea-ps

CellChatDB.use <- CellChatDB # simply
which(CellChatDB.use[["interaction"]]$ligand == "H2-BI") # 1887

CellChatDB.use[["interaction"]] <- CellChatDB.use[["interaction"]][-1887,]

which(CellChatDB.use[["interaction"]]$ligand == "H2-Ea-ps") #1900
CellChatDB.use[["interaction"]] <- CellChatDB.use[["interaction"]][-1900,]

cellchat.iso@DB <- CellChatDB.use

cellchat.iso <- subsetData(cellchat.iso)

cellchat.iso1 <- identifyOverExpressedGenes(cellchat.iso)

Error in genes.de[[i]] : subscript out of bounds

cellchat.iso <- identifyOverExpressedInteractions(cellchat.iso) ##working

Please give a clear solution on how to solve the problem.

thank you!

[songeric1107]

I find the problem; there is a typo in the identities to use. problem fixed.