Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2
Bibliographic record
Abstract
Abstract In high-throughput sequencing (HTS) studies, sample-to-sample variation in sequencing depth is driven by technical factors, and not by variation in the scale (size) of the biological system. Typically a statistical normalization removes unwanted technical variation in the data or the parameters of the model to enable differential abundance analyses. We recently showed that all normalizations make implicit assumptions about the unmeasured system scale and that errors in these assumptions can dramatically increase false positive and false negative rates. We demonstrated that these errors can be mitigated by accounting for uncertainty using a scale model, which we integrated into the ALDEx2 R package. This article provides new insights focusing on the application to transcriptomic analysis. We provide transcriptomic case studies demonstrating how scale models, rather than traditional normalizations, can reduce false positive and false negative rates in practice while enhancing the transparency and reproducibility of analyses. These scale models replace the need for dual cutoff approaches often used to address the disconnect between practical and statistical significance. We demonstrate the utility of scale models built based on known housekeeping genes in complex metatranscriptomic datasets. Thus this work provides guidance on how to incorporate scale into transcriptomic data sets.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.006 | 0.017 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".