Feature Request: pseudoBulkDGE for Non-Integer Batch-corrected Data

MarioniLab / scran

Clone of the Bioconductor repository for the scran package.

https://bioconductor.org/packages/devel/bioc/html/scran.html

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Feature Request: pseudoBulkDGE for Non-Integer Batch-corrected Data #120

Open DarioS opened 3 weeks ago

DarioS commented 3 weeks ago

Some algorithms, such as RUV-III-NB, take integer counts as input and also output integer counts in gene space whereas others, such as scMerge, will produce logarithmic scale decimal numbers in gene space. May pseudoBulkDGE support this via a moderated t-test?

LTLA commented 3 weeks ago

Hm. While technically possible, I don't think highly of performing DE directly on batch-corrected values, either in bulk or in single-cell settings. I daresay it's even worse in single-cell as most of the popular batch correction algorithms are rather... aggressive. Nonetheless, if you have a good reason to do this, I'm happy to consider a PR.

DarioS commented 2 weeks ago

Ah, O.K. Perhaps the guardrail is beneficial. This leads me to wonder if scater has a saturation plot for cancer studies.