how to analyze scRNA-seq from treatment and control
I have 4 groups scRNA-seq, inculding WT, mutant,WT+drug treatment, and mutant+durg treatment. I pooled all samples together and anlayzed the data with Seurat, I used marker genes to defined cell types. Next, I analyzed the scRNA-seq separately, but I found that several marker genes were not differentially expressed in some clusters. Now I am not sure which one is better to analyze that data. Best,
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So, what's your question? It's not clear.
do I need to merge expression matrix from each group before clustering?
That depends on whether you're interesting in comparing between the groups or not. It sounds like, yes, you probably are, so I would merge them. Providing additional details about what you've done, the output you're getting, and what you expect to see would help us answer more appropriately.
yes. I want to compare the difference between groups