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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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Issue with TransCommuProfile step 5 softmax for ligand #25

Open LaviCor opened 2 years ago

LaviCor commented 2 years ago

Hi all,

I am running into an issue when trying to follow along the instructions to analyse ligand-receptor interactions using CellCall. when running the "TransCommuProfile" command, I am faced with the error: "Error in expr_mean[intersect(ligand_symbol, detect_gene), ] : incorrect number of dimensions".

my console output looks like this: image

I am using mouse scRNAseq data analysed previously in Seurat, (I used the following code to create the CellCall object: "scLR <- CreateObject_fromSeurat(Seurat.object= sc, data_source="UMI", Org = 'Mus musculus')" )

Would really appreciate any help or insights!

TangBluebird commented 2 years ago

I got the exact same error as you! I don't think it's a species problem, because I'm using human data, and the error is also reported. Also it's not a question of method.If you solve this problem, can you tell me how to solve it?I would be grateful.

qi603 commented 2 years ago

Same here. Please let me know if you already find the solution. many thanks!

shangguansuyan commented 8 months ago

老铁，第一步CreateObject_fromSeurat函数中cell_type=什么你们没有选对，先head一下你们的seurat对象看看细胞类型在哪一列，再在cell_type=中填入列名。这样运行的结果再在TransCommuProfile函数中运行才不会报错。