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I am running CellChat on two different cohorts, AML and healthy. After merging the datasets, I performed a differential analysis using the following commands with group.DE.combined set to both TRUE and FALSE:
After that, I filtered for significant interactions and pulled upregulated ligands and receptors separately for AML. I then repeated this process for downregulated interactions in the healthy cohort:
Expectation: I expected to see the interactions_IDs (including the signaling cell types) that are upregulated in AML to be downregulated in the healthy cohort, but this isn't the case. Instead, I get completely different interaction IDs between the two conditions.
Hello,
I am running CellChat on two different cohorts, AML and healthy. After merging the datasets, I performed a differential analysis using the following commands with group.DE.combined set to both
TRUE
andFALSE
:After that, I filtered for significant interactions and pulled upregulated ligands and receptors separately for AML. I then repeated this process for downregulated interactions in the healthy cohort:
Additionally, I create a column containing source and the target cell types.
Expectation: I expected to see the interactions_IDs (including the signaling cell types) that are upregulated in AML to be downregulated in the healthy cohort, but this isn't the case. Instead, I get completely different interaction IDs between the two conditions.
Question: Does this result make sense, or am I missing something in this context? Any insights or advice would be appreciated!
Thanks
Muhammet
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