Table 1.

Summary of parameters in ProMix, Model (1). The interpretation of variable indices is as follow: G: number of proteins; L: number of specimens; K: number of samples; R: number of blocks.

Variable	Interpretation	Shared across	Index: {range}	Fixed/Random effects
$Y_{gk}$	Observed abundance of protein $g$ in sample $k$.	None. Individual data point.	$g:\{1:G\}$ $k:\{1:K\}$	NA
${\mu }_g$	Mean abundance; protein-specific	All measurements on a protein	$g:\{1:G\}$	Fixed
${\alpha }_k$	Sample effects	All proteins in a sample (channel)	$k:\{1:K\}$	Fixed
${\gamma }_{gl}$	Specimen effects; protein-specific	All replicates of a biospecimen	$g:\{1:G\}$ $l:\{1:L\}$	Fixed
$b_{g{r}_k}$	Block effects; protein-specific. $b_{g{r}_k}\sim \mathrm{N}(0,{\varphi }_g)$	All channels in a block	$g:\{1:G\}$ $r_k:\{1:R\}$	Random
$e_{gk}$	Residual error, $e_{gk}\sim \mathrm{N}(0,{\sigma }_g^2)$	None.	$g:\{1:G\}$ $k:\{1:K\}$	Random