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Teichlab / cellphonedb

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The barcodes changes when using data.frame #312

Closed chenxofhit closed 3 years ago

chenxofhit commented 3 years ago

test_counts <- as.matrix(dha.subset@assays$RNA@data) head(test_counts) then it ouputs:

image

and : test_counts <- as.matrix(dha.subset@assays$RNA@data) test_counts <- data.frame(Gene=rownames(test_counts), test_counts,stringsAsFactors = F) I append the first column named Gene for further mice gene name transferring to human gene name in my case. head(test_counts) then it outputs: image

When looking carefully, the cell barcodes changes from AAACCCAAGGAGTATT-1_3 to AAACCCAAGGAGTATT.1_3, what causes this result? Maybe the issue should not be here, but I wonder if anyone know.

prete commented 3 years ago

Hi @chenxofhit I fail to see how this issue relates to CellPhoneDB, could you explain?

chenxofhit commented 3 years ago

Yes，this issue does not relate to this topic. This issue occurs when I conduct an experiment with CellPhoneDB. I also attach a link to the Seurat repository.

chengying33 commented 2 years ago

Yes，this issue does not relate to this topic. This issue occurs when I conduct an experiment with CellPhoneDB. I also attach a link to the Seurat repository.

I got the same problem. Did you fix it then?

chenxofhit commented 2 years ago

Yes，this issue does not relate to this topic. This issue occurs when I conduct an experiment with CellPhoneDB. I also attach a link to the Seurat repository.

I got the same problem. Did you fix it then? please see: https://github.com/satijalab/seurat/issues/4492#issuecomment-846012590