A problem with a error message in identifyOverExpressedGenes in CellChat.

[weichloe]

Hi @sqjin,
Fantastic work and package. I am a novice at using R programming. I encountered a problem when I use the function: identifyOverExpressedGenes in CellChat.
After looking in the web, I confirmed I did the subsetData and checked `object@data.signaling.
I found my data.signaling matrix only has 2 x 2252. It looks like the gene names are disappeared. How did I solve this problem?
I am looking forward to your response.
Thank you so much for your help.

The error message is shown as bellows.

Mouse.cellchat <- subsetData(Mouse.cellchat)
Mouse.cellchat <- identifyOverExpressedGenes(Mouse.cellchat)
Error in identifyOverExpressedGenes(Mouse.cellchat) :
Please check object@data.signaling and ensure that you have run subsetData and that the data matrix object@data.signaling looks OK.
Mouse.cellchat@data.signaling
2 x 2252 sparse Matrix of class "dgCMatrix"
[[ suppressing 54 column names ‘AAACCCACAATACAGA-1_1’, ‘AAACCCACATGAATCC-1_1’, ‘AAACCCACATTGCTGA-1_1’ ... ]]

F2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.6931472 . . . . . . . . . . . . . . . . . . . . . .
C3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

F2 ......
C3 ......

.....suppressing 2198 columns in show(); maybe adjust 'options(max.print= *, width = *)'
..............................

[sqjin]

@weichloe It is surprising that there are only two rows in your data. Can you show me the codes related to the database?

[weichloe]

Hi @sqjin,
Thanks so much for your reply. I re-created the metadata and re-run the CellChatDB. The problem seems to be resolved.
But the mouse CellChatDB still has the following genes ( H2-Q8 H2-T9 H2-T18 H2-Q9 H2-L H2-BI H2-D H60a H2-Ea-ps )
in our data matrix not to be identified.

weichloe

#Set the ligand-receptor interaction database
CellChatDB<- CellChatDB.mouse
showDatabaseCategory(CellChatDB)

use all CellChatDB for cell-cell communication analysis

CellChatDB.use <- CellChatDB # simply use the default CellChatDB

Mouse.cellchat@DB <- CellChatDB.use
Mouse.cellchat <- subsetData(Mouse.cellchat)

Issue identified!! Please check the official Gene Symbol of the following genes:
H2-Q8 H2-T9 H2-T18 H2-Q9 H2-L H2-BI H2-D H60a H2-Ea-ps

future::plan("multiprocess", workers = 4) # do parallel
Mouse.cellchat <- identifyOverExpressedGenes(Mouse.cellchat)
Mouse.cellchat<- identifyOverExpressedInteractions(Mouse.cellchat)
Mouse.cellchat <- projectData(Mouse.cellchat, PPI.mouse)

Mouse.cellchat@data.signaling
639 x 2252 sparse Matrix of class "dgCMatrix"
[[ suppressing 53 column names ‘AAACCCACAATACAGA-1_1’, ‘AAACCCACATGAATCC-1_1’, ‘AAACCCACATTGCTGA-1_1’ ... ]]
[[ suppressing 53 column names ‘AAACCCACAATACAGA-1_1’, ‘AAACCCACATGAATCC-1_1’, ‘AAACCCACATTGCTGA-1_1’ ... ]]

Epha4 . . . . . . . . 0.6931472 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lamc2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lamc1 . 1.609438 . . . 1.609438 . . 1.0986123 . . . 0.6931472 . . . . . . . . . . . . . . . . . . . . . 1.098612 .
Col4a4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Inhbb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lefty2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lefty1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Angptl1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Il17f . . . . . . . . . . . . . . . 0.6931472 . . . . . . . . . . . . . . . . . . . .

Epha4 . . . . . . . . . . . 1.3862944 . . . . . ......
Lamc2 . 0.6931472 . . . . . . . . . 0.6931472 . . . . . ......
Lamc1 1.098612 . . 1.098612 . . 1.098612 . . . . 1.0986123 . . . 0.6931472 . ......
Col4a4 . . . . . . . . . . . . . . . . . ......
Inhbb . . . . . . . . . . . . . . . . . ......
Lefty2 . . . . . . . . . . . . . . . . . ......
Lefty1 . . . . . . . . . . . . . . . . . ......
Angptl1 . . . . . . . . . . . . . . . . . ......
Il17f . . . . . . . . . . . . . . . . . ......

..............................
........suppressing 2199 columns and 621 rows in show(); maybe adjust 'options(max.print= *, width = *)'
..............................
[[ suppressing 53 column names ‘AAACCCACAATACAGA-1_1’, ‘AAACCCACATGAATCC-1_1’, ‘AAACCCACATTGCTGA-1_1’ ... ]]

Lrp5 . . . . . . . . . . . . . . . . . . . . 0.6931472 . . . 0.6931472 .
Nrxn2 . . . . . . . . . . . . . . . . . . . . . . . . . .
Entpd1 . . . . 1.609438 . . 1.098612 . . . . . . . . . . 0.6931472 . . . . 1.098612 . .
Sfrp5 . . . . . . . . . . . . . . . . . . . . . . . . . .
Sema4g . . . . . . . . . . . . . . . . . . . . . . . . . .
Fgf8 . . . . . . . . . . . . . . . . . . . . . . . . . .
Anxa1 . . . . . . . . . . . . . . . . . . . . . . . . . .
Clcf1 . . . . . . . . . . . . . . . . . . . . . . . . . .
Vegfb . . . . . . . . 0.6931472 . . . . . . . . . . . . 1.098612 . . . .

Lrp5 . . . 0.6931472 . . . . . 1.098612 . . . . . . . . . . . . .
Nrxn2 . . . . . . . . . . . . . . . . . . . . . . .
Entpd1 0.6931472 . . 1.3862944 . . . . . . 1.098612 1.3862944 . . 0.6931472 . . . . . . . .
Sfrp5 . . . . . . . . . . . . . . . . . . . . . . .
Sema4g . . . . . . . . . . . 0.6931472 . . . . 0.6931472 . 0.6931472 . . . .
Fgf8 . . . . . . . . . . . . . . . . . . . . . . .
Anxa1 . . . . . . . . . . . . . . . . . . . . . . .
Clcf1 . . . . . . . . . . . . . . . . . . . . . . .
Vegfb . . . . . . . . . 1.098612 . . . 1.098612 . . . . . . . . .

Lrp5 0.6931472 . . . ......
Nrxn2 . . . . ......
Entpd1 . . . . ......
Sfrp5 . . . . ......
Sema4g . . . . ......
Fgf8 . . . . ......
Anxa1 . . . . ......
Clcf1 . . . . ......
Vegfb . . . . ......

[sqjin]

@weichloe I think there are some issues for these gene names. I will fix them in the next version. If you are really concerned about these gene names, you can manually correct these gene names.

[Yijia-Jiang]

I cannot run identifyOverExpressedGenes function, so I run manually and get error: Error in (function (cl, name, valueClass) :
assignment of an object of class “character” is not valid for @‘var.features’ in an object of class “CellChat”; is(value, "list") is not TRUE. Any suggestions on how to deal with this?

[sqjin]

@aj088 I suggest to check your input data including both data matrix and cell labels.

[wdg118]

@sqjin I have a similar issue to @weichloe

I ran the source code for identifyOverExpressedGenes, and I get the error:

Error in (function (cl, name, valueClass) : assignment of an object of class “character” is not valid for @‘var.features’ in an object of class “CellChat”; is(value, "list") is not TRUE
Traceback:

1. identifyOverExpressedGenes(cellchat)
2. (function (cl, name, valueClass)
   . {
   . ClassDef <- getClass(cl)
   . slotClass <- ClassDef@slots[[name]]
   . if (is.null(slotClass))
   . stop(gettextf("%s is not a slot in class %s", sQuote(name),
   . dQuote(cl)), domain = NA)
   . if (.identC(slotClass, valueClass))
   . return(TRUE)
   . ok <- possibleExtends(valueClass, slotClass, ClassDef2 = getClassDef(slotClass,
   . where = .classEnv(ClassDef)))
   . if (isFALSE(ok))
   . stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, "%s") is not TRUE",
   . dQuote(valueClass), sQuote(name), dQuote(cl), slotClass),
   . domain = NA)
   . TRUE
   . })(structure("CellChat", package = "CellChat"), "var.features",
   . "character") # at line 38 of file
3. stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, "%s") is not TRUE",
   . dQuote(valueClass), sQuote(name), dQuote(cl), slotClass),
   . domain = NA)

I then inspected cellchat@var.features:

Extract cell-level features

cell_features <- cellchat@var.features

Print the number of cell-level features

print(length(cell_features)

and got:

[1] 0

So for some reason I have no features.

I also ran View(cellchat@data.signaling) and got:
2 x 30807 sparse Matrix of class "dgCMatrix"

where my genes disappeared

I read in a Seurat object and followed the tutorial to make a cellchat object.

[AHerik]

Hi @weichloe how did you re-create your meta data? I have the exact same problem as you, only 2 rows of genes (C3 and F2).

[PXYXYXY]

Hi @sqjin,
Fantastic work and package. I am a novice at using R programming. I encountered a problem when I use the function: identifyOverExpressedGenes in CellChat.

I had run “cellchat = subsetData(cellchat) ”

but，then when I run ”str(cellchat@data.signaling)“

there is
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
..@ i : int(0)
..@ p : int [1:8308] 0 0 0 0 0 0 0 0 0 0 ...
..@ Dim : int [1:2] 0 8307
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : num(0)
..@ factors : list()
Thank you so much for your help.

[sqjin]

@PXYXYXY It seems that you did not use the correct input data matrix or the L-R database such as human or mouse