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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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Ligands and receptor of the pathway were expressed, but it can't be detected through cellchat #250

Open Emily-Y21 opened 3 years ago

Emily-Y21 commented 3 years ago

I met a problem when using CellChat. I wanted to know whether the CLEC pathway existed in my data. First, I analyzed the expression of the ligand and receptor of this pathway in my data and found that ligands(CLEC2B, CLEC2C, CLEC2D) were expressed in my data.However, only CLEC2C-KLRB1 and not CLEC2B-KLRB1 were detected in the communication analysis. I would like to ask why and how to solve it.

sqjin commented 3 years ago

@Emily-Y21 This might be related with the method for computing average expression per cell group. You can try the "truncatedMean". For example, cellchat <- computeCommunProb(cellchat, type = "truncatedMean", trim = 0.1)

Emily-Y21 commented 3 years ago

Thanks. I've solved the problem by running cellchat <- computeCommunProb(cellchat, type = "truncatedMean", trim = 0.1).

------------------ 原始邮件 ------------------ 发件人: "sqjin/CellChat" @.>; 发送时间: 2021年7月19日(星期一) 凌晨2:23 @.>; @.**@.>; 主题: Re: [sqjin/CellChat] Ligands and receptor of the pathway were expressed, but it can't be detected through cellchat (#250)

@Emily-Y21 This might be related with the method for computing average expression per cell group. You can try the "truncatedMean". For example, cellchat <- computeCommunProb(cellchat, type = "truncatedMean", trim = 0.1)

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