Comments (4)
sqjin
commented on July 23, 2024
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!
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AHerik
commented on July 23, 2024
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!
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heleof23
commented on July 23, 2024
@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.
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AHerik
commented on July 23, 2024
@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!
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Related Issues (20)
- Error netVisual_heatmap() on a merged object from Seurat
- netAnalysis_signalingRole_network cluster.cols and cluster.rows not working HOT 1
- error with identifyOverExpressedGenes(cellchat) HOT 1
- Error in if (dim(prob)[3] <= 25) { : argument is of length zero HOT 2
- NetP empty after running computeCommunProb HOT 1
- Missing Column `annotation` in LRsig after merge cellchat and celltalk L-R pair
- parameter "group.by" in subsetCellChat doesn't work
- Issue with installing CellChat package in R studio HOT 1
- Why haven't we utilized single-cell proteomics for cell communication recognition and prediction? HOT 1
- Error in createCellChat object
- [email protected] 0 x 12257 sparse Matrix of class "dgCMatrix" HOT 2
- rankingsimilarity - back to issue #160 HOT 1
- unused arguments (min.dist = 0.3, n.neighbors = k) HOT 1
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