Simulation of microarray data with realistic characteristics

BMC Bioinformatics

Table 3 List of hybridization parameters. Overview of the hybridization effect parameters.

$H_{σ^{2}}$	Multiplicative Gaussian hybridization noise variance. Hybridization noise is drawn from N (0, $H_{σ^{2}}$ ).
H _errors	If set, hybridization errors are included in simulation.
H _bgnoise	Percent of the intensity values covered by the background noise.
H _bgvar	Background noise variance, relative to background noise mean determined using H_bgnoise.
H _bggrad	Gradient (noise pattern) for background noise.
H _noscratch	Number of scratches on the slide.
H _slength	Maximum length of the scratch, scratch length is drawn from U (0, H_Slength).
H _Swidth	Width of the scratch.
H _noair	Number of air bubbles visible on the slide.
$H_{μ_{a i r}}$	Mean for the air bubble radius, drawn from N (μ_air, $σ_{a i r}^{2}$ ).
$H_{σ_{a i r}^{2}}$	Allowed variation (variance) for air bubble size radius.
H _bleed	Percent of spots having dye outside spot area (bleeding).
H _bleedsize	Size of the spot bleed (how many times the spot size).
H _bleeddist	How far from the origin the bleeding goes.

ISSN: 1471-2105