computeCommunProb :Error in data.use[RsubunitsV, ]

[wulc21]

Hi dear professor, could you help me solve the problem? Thank you very much
cellchat <- computeCommunProb(cellchat)
Error in data.use[RsubunitsV, ] : 下标出界

[sqjin]

Hi @wulc21, I have no idea on this issue except that I can replicate your error. If you can share me your CellChat object, I am happy to test it; otherwise, you can try the source codes line by line to figure out the reason.

[DawnEve]

I encounter the same issue.

cellchat2 <- computeCommunProb(cellchat2)

Error in data.use[RsubunitsV, ]: subscript out of bounds
Traceback:

1. computeCommunProb(cellchat2)
2. computeExpr_complex(complex_input, data.use, complex)
3. my.sapply(X = 1:nrow(Rsubunits), FUN = function(x) {
 .     RsubunitsV <- unlist(Rsubunits[x, ], use.names = F)
 .     RsubunitsV <- RsubunitsV[RsubunitsV != ""]
 .     return(geometricMean(data.use[RsubunitsV, ]))
 . })
4. pblapply(X = X, FUN = FUN, ..., cl = cl)
5. lapply(X, FUN, ...)
6. FUN(X[[i]], ...)
7. geometricMean(data.use[RsubunitsV, ])
8. nrow(x)

[sqjin]

@DawnEve Can you please make sure there is no obvious issue of the following four parts: 1) Use the correct CellChatDB: either mouse or human; 2) Please check the input data matrix cellchat@data; 3) Please check the subset data matrix cellchat@data.signaling; 4) Please check the cell group information is correct: unique(cellchat@idents).

[alhadjil]

@DawnEve Can you please make sure there is no obvious issue of the following four parts: 1) Use the correct CellChatDB: either mouse or human; 2) Please check the input data matrix cellchat@data; 3) Please check the subset data matrix cellchat@data.signaling; 4) Please check the cell group information is correct: unique(cellchat@idents).

Hi,

I've used following code on an Seurat scRNASeq object and I still get the same Error message

data.input <- GetAssayData(dataset, assay = "RNA", slot = "data") # normalized data matrix
Idents(object = dataset) <- 'Named'
labels <- Idents(dataset)
identity <- data.frame(group = labels, row.names = names(labels)) # create a dataframe of the cell labels
cellchat <- createCellChat(data = data.input)
cellchat <- addMeta(cellchat, meta = identity, meta.name = "labels")
cellchat <- setIdent(cellchat, ident.use = "labels") # set "labels" as default cell identity
CellChatDB <- CellChatDB.mouse # use CellChatDB.human if running on human data
CellChatDB.use <- subsetDB(CellChatDB, search = "Secreted Signaling")
cellchat@DB <- CellChatDB.use # set the used database in the object
cellchat <- subsetData(cellchat) # subset the expression data of signaling genes for saving computation cost
future::plan("multiprocess", workers = 8) # do parallel
cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)
cellchat <- projectData(cellchat, PPI.mouse)
groupSize <- as.numeric(table(cellchat@idents))
cellchat <- computeCommunProb(cellchat)
cellchat <- computeCommunProbPathway(cellchat)

Then I followed the recommended steps and I got following results:

(1) I'm using the MouseDB and my scRNASeq dataset is from mice
(2) cellchat@data

(3) cellchat@data.signaling

(4) unique(cellchat@idents)

Can you please help me? Thanks!

[zpingfeng]

should the unique(cellchat@idents) be the cluster names?

I have 1) Use the correct CellChatDB: mouse ; 2) the input data matrix cellchat@data, range from 0.00000 to 8.34498, dimension 14393 x 2814 ; 3) the data matrix cellchat@data.signaling, range from 0.00000 to 8.34498, dimension 3000 x 2814; 4) the cell group information is correct: unique(cellchat@idents): 1 to 11.

I still got similar error message
cellchat <- computeCommunProb(cellchat)
Error in data.use[RsubunitsV, ]: subscript out of bounds

[wfma]

I ran into this error also. I found that I used the wrong idents from Seurat!

[ysuzuki1978]

I am having the same error, please tell me how to fix the idents from Seurat to solve the problem.

[Xiujia-Yang]

Perhaps the following two steps were missed,

cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)

This issue mentioned above was solved for me when the two steps were executed beforehand.

[dmj6288]

Hi All,

It is because the RSubunitsV variable is NULL. This happens when the cellchat@LR slot is empty. In other words, CellChat was unable to identify any relevant Ligand-Receptor pairs in the gene list you provided. This slot get's populated when you run identifyOverExpressedInteractions(). I recommend increasing the gene list (rownames or relax some upstream filtering pipeline) you provided and then it will work.

Best,
dmj

[codecant1]

@dmj6288 @sqjin Hello -- having similar difficulty with this step (Error in data.use[RsubunitsV, ]: subscript out of bounds). Confirmed that the cellchat@LR slot is empty, even after running identifyOverExpressedInteractions().

Gene list constituent of 50K+ HUGO symbols. Running with bulk samples (N=61), in accordance with previous mention by @sqjin that such analysis is possible with CellChat despite its single cell intentions.

Kindly find my cellchat object attached
cellchat.zip

Any insight is greatly appreciated.

[dmj6288]

I believe it is possible to run bulk samples with cellchat, but when I run cellchat on bulk data, I've always received a very small number of LR interactions.

[imrjesh]

There must be some issue with your dataset.

[patrycja-oleniacz]

I had similar error (Error in data.use[RsubunitsV, ] : subscript out of bounds) when I forgot to run:

cellchat <- updateCellChat(cellchat)

before
identifyOverExpressedGenes(cellchat)
identifyOverExpressedInteractions(cellchat)

Running cellchat <- updateCellChat(cellchat) before those two commends solved the problem in my case

[zyc0321]

I had similar error (Error in data.use[RsubunitsV, ] : subscript out of bounds) when I forgot to run:

cellchat <- updateCellChat(cellchat)

before identifyOverExpressedGenes(cellchat) identifyOverExpressedInteractions(cellchat)

Running cellchat <- updateCellChat(cellchat) before those two commends solved the problem in my case

Problem solved! Thanks so much!!