Entering edit mode
1 day ago
Lee
•
0
Hello,
I'm currently running a single cell analysis, and I have question that I would like to check whether it makes sense statistically, or maybe I'm missing something.
So in Seurat we can do differential expression (DE) analysis between clusters (Cluster1 vs Cluster2) or within Clusters (Cluster1_Ctrl vs Cluster1_Treated). That's all good.
However the user keeps requesting for a cluster subset vs another cluster subset DE analysis, e..g
- Cluster1_Ctrl vs Cluster2_Ctrl
- Cluster1_Treated vs Cluster2_Treated
I've tried searching here and other places but couldn't find anything. Does this make sense, statistically? If not, why? Or is there a way to run this kind of analysis in Seurat that I'm missing?
Thank you in advanced for your help and opinions!
Here are some past threads that would be useful :
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
scRNA-seq: How does cell number in clusters affect the number of DE genes?
Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
scRNAseq Differential expression analysis
https://bioconductor.org/books/3.21/OSCA.multisample/multi-sample-comparisons.html#creating-pseudo-bulk-samples
Thank you, I will check out the links. Although I'm not certain that pseudobulking is the issue here, I've run DE pseudobulking before. What I haven't tried is what the user is requesting, comparing a subset of Cluster1 vs a subset of cluster2.
Thanks for clarifying. I missed the "subset" part from your question. What criteria will you be using to subset the data? Can you share the basis of this odd request.
It's just as it is. Actually it's not Ctrl vs Treated - it's Wild Type vs Mutant. Almost each cluster contain an overlap of WT and Mutant cells.
The user just really really wants to compare cells Cluster1_WT vs Cluster2_WT, and same for Mutant.
I think I've come up with a possible solution. Split the seurat object into 2 - "WT" and "Mutant". Then run clustering separately for each object. After that the user can compare Cluster1 vs Cluster2 as much as they want.