Thank you! I'll look into those chapters.
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DE Analysis on Scran-Normalized Counts
I would like to perform differential expression analysis on a scRNA-sequenced GEO dataset (GSE111065). I can use either raw counts from featureCounts, or normalized counts prepared via the deconvolution method in scran. I would like to use the normalized counts if possible, but am unsure if I can use them as input into programs like Seurat. I'm interested in figuring our how a few very specific genes change between cells of different types.
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lucia.liu54 •
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lucia.liu54 •
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If you're already using scran, why don't you just use Bioconductor packages for your DE as described in the OSCA book? Chapters 11 and 14 may be of particular interest to you.
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