Hello,
This is a general question with no specific example concerning differential gene expression analysis in scRNAseq data.
We sometimes want to compare two conditions in our DE** analysis but we see the the sample size of these groups greatly differ.
For example, we compare control (n=1500 cells) vs LPS (n=240 cells).
Someone suggested to me to downsample the cells, so at the end one would have a similar / equal number of cells in each group.
I didn't find any information whehter this is something that is acceptable to do, and I am a bit unsure about the approach, or how I can perform it well, or whether there's a nother way to perform the comparison.
I would greatly appreciate any ideas/comments/suggestions !
** We perform DE analysis using FindMarkers/FindAllMarkers functions in Seurat with Wilcoxon Rank Sum test.
1 answer
I would avoid downsampling as you might remove some interesting data.
In your case, I would use a pseduobulk approach, using AggregateExpression.
If you want to use FindMarkers, you cna set return.seurat =TRUE otherwise, you can use those aggregated counts in DESeq2 or edgeR
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