Table 2 List of slide parameters. Overview of the slide simulation parameters. More detailed documentation of the parameters is available on the companion web page [19].

S _spot

Model used for the spot: circle, Gaussian, hyperbolic.

S _pix

Maximum width/height of the area for the spot in pixels.

S _movprob

Probability for a spot to drift (move) from designated location. This parameter models random movement. See parameter B _curve for systematic drift.

S _mov

Maximum allowed movement bias from designated location, movement in x-axis S _x and y-axis S _y are drawn from uniform distribution U (-S _mov , S _mov ).

S _μ

Mean radius of the simulated spot. Spot radius is drawn from N (S _μ , $S_{{\sigma }^2}$) distribution.

$S_{{\sigma }^2}$

Allowed variation (variance) of the spot size.

P

If set, print tip leaves a mark to the spot.

P _p

Probability for print tip mark to be visible in a spot.

P _h

Maximum height of the print tip mark, print tip height is drawn from U (0, P _h ) distribution.

P _w

Maximum width of the print tip mark, print tip width is drawn from U (0, P _w ) distribution.

P _b

Maximum of how much print tip mark is allowed to drift from spot center. Movement in x-axis P _x and y-axis P _y are drawn from U (-P _b , P _b ).

C _prob

Probability for a spot to suffer from a chord cut.

C _num

Maximum number of chord cuts from a spot.

C _cut

Maximum depth of the chord cut, cut depth is drawn from U (0, C _cut ).

N _slides

Number of slides to be generated.

N _time

Time points when slides are made. This is relevant only for time series data.

N _channels

Number of channels (different dyes) on the slide.

N _spots

Total number of spots on the slide.

N _height

Number of rows of spots on the slide.

N _width

Number of columns of spots on the slide.

B

Subarray layout on the slide i.e. number of (subarray)rows and (subarray)columns.

B _space

Space between individual subarrays on the slide.

B _curve

Parameter used to control the subarray curving (i.e. systematic drift in spot printing).

B _maxc

Maximum distance the bin is allowed to curve, curvature parameter is drawn from U (0, B _maxc ).

B _spots

Number of spots in each subarray.

B _height

Number of rows in subarrays.

B _width

Number of columns in subarrays.