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Table 1 DEG Methods for Single-Subject Studies and their previous validations

From: Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine

Method Experimental Design Distribution Assumptions P-value Validation of method for single subject inference in original methods publications
Internal External
Simulation Biological Replicates or Gold Standard Translation to diagnosis, prognosis & treatment
edgeR [21] r NB a
DESeq [22] r NB a
DESeq2 [23] r NB a
DEGseq [24] r B a
NOISeqa [15] r/ss (as NOISeq-sim) NP a ±b
Mixture Model [5] ss MM ±c
iDEG [14] ss NB a
  1. NB Negative Binomial, B Binomial, NP Non-Parametric, MM Mixture Model, ss single-subject analytics, r analytics of between group of replicates, = completed, ± = partially addressed, ✗ = not addressed
  2. aNOISeq-Bio was used to construct the reference standard, while NOISeq-sim was used in the single-subject prediction sets
  3. bPartial validation conducted using qPCR with 400 genes with ~ 80% DEGs
  4. cMixture Model provides a posterior probability rather than a p-value, when FDR < 5% is indicated in the manuscript, it translates as a posterior probability > 95% for the mixture models