New paper in Genome Biology! genomebiology.biomedcentral.com/articles/10.... We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load). - ThreadSky

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inschool4life.bsky.social • 32 days ago

New paper in Genome Biology!

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03609-3

We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).

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ggloor.bsky.social•30 days ago

awesome to see it out

inschool4life.bsky.social•32 days ago

Traditional normalization methods often make implicit assumptions abou thte biological system's scale, such as microbial load or total RNA content. These assumptions can lead to false positives and negatives.

inschool4life.bsky.social•32 days ago

We present scale mdoels, which extend normalization by modeling potential errors in these assumptions (reducing false positives), or by allowing researchers to make more biologically plausible assumptions (reducing false negatives).

inschool4life.bsky.social•32 days ago

In real data analysesd simulation studies we find our methods often lead to dramatic decreases in false positves (FDR can drop from >75% to a nominal 5%) while simultaneously maintaining or improving statistical power.

inschool4life.bsky.social•32 days ago

To facilitate adoption, we've update the popular ALDEx2 software package on Bioconductor to support scale model analysis.

inschool4life.bsky.social•32 days ago

We are also developing a new ALDEx3 library that is about 1000 times faster than ALDEx2 with a streamlined user interface (although its still in beta I am using it regularly)
https://github.com/jsilve24/ALDEx3

inschool4life.bsky.social•32 days ago

Scale models are not just heuristics but have a rich theoretical foundation based on Bayesian Partially Identified Models. That theory is presented here:

https://arxiv.org/abs/2201.03616

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