Question: How does AverageExpression() and aggregateData() differ from each other?
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gravatar for Researcher
5 weeks ago by
Researcher60
Researcher60 wrote:

Can someone please explain how does Seurat's AverageExpression() differ from muscat's aggregateData() and which one is better to get average expression of genes for each cluster?

Thanks in advance.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Researcher60
0
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

Hey Researcher,

The difference between these two functions can be easily determined by just reading the manual page entries:

I trust that you can now make your own decision in relation to your own experiment and data.

Best wishes, Kevin

ADD COMMENTlink written 5 weeks ago by Kevin Blighe65k

Hi Kevin, Thanks for sharing these links here. Actually I didn't ask my question clearly. My doubt is Seurat's AverageExpression() should exactly be the same as muscat's aggregateData() with fun="mean". As both are just the average gene expression values from a group of cells from each of the identified cell-type or cluster. But when I checked it in my data, it was not the case. May be I am getting it completely wrong. Can you please correct me if I am missing something?

Thanks!

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Researcher60

This is likely a question that no general user can answer. You would have to look through the code for both functions, or just ask the respective authors directly. One thing is for sure: expect the unexpected in bioinformatics. There is no regulation in this field.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Kevin Blighe65k
1

That's true. I'll write to them. Thanks!

ADD REPLYlink written 5 weeks ago by Researcher60
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