Skip to main content

Table 1 Models and parameters for synthetic data generation

From: Joint between-sample normalization and differential expression detection through 0-regularized regression

ieunif(5,10)length of gene i
\(\alpha _{i} \sim \mathcal {N}(0,1)\)other log scaling factors of gene i
βi=0log-fold change for non-DE genes
\(\beta _{i} \sim \mathcal {N}(2,1)\)log-fold change for up-regulated DE genes
\(\beta _{i} \sim \mathcal {N}(-2,1)\)log-fold change for down-regulated DE genes
\(x_{j} \sim \mathcal {N}(0,1)\)covariates for sample j
Njunif(2,3)×106library size of sample j
\(d_{j} \sim \mathcal {N}(0, 1)\)other log scaling factors of sample j
\(\mu _{ij} = N_{j} \frac {\ell _{i}}{\sum _{i=1}^{m} \ell _{i}} \mathrm {e}^{\alpha _{i} + \beta _{i} x_{j} + d_{j}}\)mean read counts of gene i in sample j