Question: how to analyze scRNA-seq from treatment and control
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gravatar for hubenxia123
5 months ago by
hubenxia1230 wrote:

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,

next-gen • 271 views
ADD COMMENTlink written 5 months ago by hubenxia1230

So, what's your question? It's not clear.

ADD REPLYlink written 5 months ago by jared.andrews075.3k

do I need to merge expression matrix from each group before clustering?

ADD REPLYlink written 5 months ago by hubenxia1230

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.

ADD REPLYlink written 5 months ago by jared.andrews075.3k

yes. I want to compare the difference between groups

ADD REPLYlink written 5 months ago by hubenxia1230
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