Table 2 Overview of parameters in the SIMAGE model. Some parameters are known (such as number of spots per grid), others should be set by the user (the flag indicates when the parameter can also be estimated from the data). Details concerning these parameters are discussed in the implementation section.

n _row

Number of grids per row

n _col

Number of grids per column

$n_{spot}^2$

Number of spots per grid

n _slide

Number of slides

n _rep

Number of technical replications

n _pin

Number of spot pins

μ

Mean expression signal

v

μ _-, μ ₊

Logratio-shift due to down- and upregulation

v

π_-, π₊

Proportion of down-, up-regulated genes

v

${\sigma }_G^2$

Variation in gene expression

v

ρ

Correlation between Cy3 and Cy5 expression

v

${\sigma }_{\epsilon }^2$

Replication variation

v

n _bg

Number of background 'densities'

σ _bg

Mean standard deviation per background density

s

Maximum slope of the linear tilt

${\sigma }_{channel}^2$

Channel variation

v

${\sigma }_{pin}^2$

Spot pin variation

v

${\sigma }_X^2$

Gene × dye variation

α ₁

Non-linearity parameter 'curvature'

v

α ₂

Non-linearity parameter 'tilt'

v

δ

Fishtailing parameter

v

w

Scanning device bias

v

n _h , n _d , n _s

Maximum number of hairs, donuts and missing spots

l _h , l _d

Maximum length of hairs and radius of donuts