data.signaling matrix error when using mouse database (Error in identifyOverExpressedGenes)

[AHerik]

Hi, I'm having an error similar to a previous user (#264). If I run CellChatDB.mouse, and I subset my cellchat object (subsetData), I get this error:

Error in identifyOverExpressedGenes(cellchat_DMSO) : 
  Please check `[email protected]` and ensure that you have run `subsetData` and that the data matrix `[email protected]` looks OK 

When I look at the data.signalling matrix of my cellchat object, I see 2 rows:

> [email protected]
2 x 10547 sparse Matrix of class "dgCMatrix"
  [[ suppressing 66 column names ‘AAACCCAAGAATTCAG-1’, ‘AAACCCACAACCCTCT-1’, ‘AAACCCACACCAGCCA-1’ ... ]]
                                                                                                                                                
C3 . . . . . . . . . .        . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.183826 . . . . . .
F2 . . . . . . . . . 2.642966 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .        . . . . . .
                    
C3 . .        ......
F2 . 0.943755 ......

 .....suppressing 10481 columns in show(); maybe adjust 'options(max.print= *, width = *)'
 ..............................

I do not get this same error when I use CellChatDB.human. How can I fix my data.signalling matrix?

Thank you for your help!

[sqjin]

If you work on the human data, you should use CellChatDB.human instead of mouse database

…

On Sun, Jun 11, 2023 at 3:50 AM AHerik ***@***.***> wrote: Hi, I'm having an error similar to a previous user (#264 <#264>). If I run CellChatDB.mouse, and I subset my cellchat object (subsetData), I get this error: Error in identifyOverExpressedGenes(cellchat_DMSO) : Please check ***@***.***` and ensure that you have run `subsetData` and that the data matrix ***@***.***` looks OK When I look at the data.signalling matrix of my cellchat object, I see 2 rows: > ***@***.*** 2 x 10547 sparse Matrix of class "dgCMatrix" [[ suppressing 66 column names ‘AAACCCAAGAATTCAG-1’, ‘AAACCCACAACCCTCT-1’, ‘AAACCCACACCAGCCA-1’ ... ]] C3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.183826 . . . . . . F2 . . . . . . . . . 2.642966 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C3 . . ...... F2 . 0.943755 ...... .....suppressing 10481 columns in show(); maybe adjust 'options(max.print= *, width = *)' .............................. I do not get this same error when I use CellChatDB.human. How can I fix my data.signalling matrix? Thank you for your help! — Reply to this email directly, view it on GitHub <#632>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHXF63GF4KWMOHH3QKZCI6LXKTFX7ANCNFSM6AAAAAAZB3Q3TQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[AHerik]

Hello Dr. @sqjin,

We are using mouse data, which is why I'm confused as to why it works with the CellChatDB.human instead.

Thank you for your swift reply, your tool is fantastic!

[heleof23]

@AHerik Hello! Were you able to resolve the issue? I can't seem to find any admin solution here, seems like i have to change the meta data.

[AHerik]

@heleof23 hello! Yes, I found the solution. In our case, it was twofold. Number one, our mouse genes were named differently from the CellChatDB gene names, and I changed the meta data to have the same format of gene names. Number two, I was actually using reindeer data in another one of our projects, and it worked when I used the human cell chat db because our gene names were orthologous with the human equivalents, and were named that way.

In short, the gene names have to match between your dataset and the cell chat dataset. Let me know if you need any help!