Power calculations for the detection of differentially expressed genes in pseudobulk scRNA-seq data
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10 days ago
Ali • 0

I'm looking to tips to help plan a scRNA-seq experiment. Specifically, how do you estimate the number of cells needed to reach a specific power using scRNA-seq between two conditions.

While it's a fairly homogeneous population (cell line comparison), we are limited to single cell analysis (and thus pseudobulk analyses), instead of bulk RNA-seq.

We are running a scRNA-seq pilot, but until that data comes through I want to do some initial calculations: I have access to bulk RNA-seq for the control line and another semi-relevant scRNA-seq dataset for a related line. What's the best approach here? Downsampling the bulk data to build an artifical scRNA-seq dataset and then a package like scPower or powsimR?

Thanks

scRNA-seq pseudobulk power RNA-seq • 256 views