How does AverageExpression() and aggregateData() differ from each other?

Question

[Researcher]

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.

Answer 1

[Kevin Blighe]

Hey Researcher,

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

• https://www.rdocumentation.org/packages/Seurat/versions/3.1.4/topics/AverageExpression
• https://rdrr.io/bioc/muscat/man/aggregateData.html

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

Best wishes, Kevin

[Researcher]

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!

[Kevin Blighe]

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.

[Researcher]

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