Hi,
I have single-cell RNA-seq data from 5 donors, and for each donor, I have one Tumor and one Non-Tumor sample. I'm working with a Seurat object that contains all the cells, and I would like to perform a paired differential gene expression (DGE) analysis comparing Tumor vs Non-Tumor conditions while accounting for the paired design (i.e., donor effect).
Do you have an idea how can I perform this analysis using Seurat’s FindMarkers function?
Thanks in advance for your help!
1 answer
If all you're interested in doing is doing tumour vs non-tumour from 5 cases then why not create a pseudobulk and just run normal DESeq2 on the resulting counts?
What do you think you'll gain by doing tumour vs normal at single-cell resolution? The whole point of single cell is to define sub-populations within the sample or group of samples. Because of the sparseness of single-cell data, you always lose power so it's important to understand why you're doing something. If you have a tumour and you're comparing it against a normal control without defining sub-populations then that's not really a single-cell experiment and you're just underpowering any results. Am I missing something?
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