How should the output count table be treated before downstream analysis?

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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How should the output count table be treated before downstream analysis? #63

Closed tkapello closed 3 years ago

tkapello commented 3 years ago

Sorry for writing as a separate "issue", but the original one was closed too quickly. My confusion is about how one should use the SoupX output. After the correction, numbers are not integers anymore. Would you recomment rounding as you describe in the vignette or using the corrected counts as they are before normalization, scaling and dimensionality reduction?

constantAmateur commented 3 years ago

If you're just using Seurat, it is fine to use a non-integer matrix as input. If you do need for counts to be integers, set roundToInt=TRUE when running adjustCounts. Or just round the resulting matrix to integers yourself.