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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.

From: SIMAGE: si mulation of DNA-m icroa rray g ene e xpression data

Parameter Description Can be estimated
n row Number of grids per row  
n col Number of grids per column  
n s p o t 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGUbGBdaqhaaWcbaGaem4CamNaemiCaaNaem4Ba8MaemiDaqhabaGaeGOmaidaaaaa@34E0@ 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
σ G 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFdpWCdaqhaaWcbaGaem4raCeabaGaeGOmaidaaaaa@30AC@ Variation in gene expression v
ρ Correlation between Cy3 and Cy5 expression v
σ ε 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFdpWCdaqhaaWcbaGae8xTdugabaGaeGOmaidaaaaa@3137@ Replication variation v
n bg Number of background 'densities'  
σ bg Mean standard deviation per background density  
s Maximum slope of the linear tilt  
σ c h a n n e l 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFdpWCdaqhaaWcbaGaem4yamMaemiAaGMaemyyaeMaemOBa4MaemOBa4MaemyzauMaemiBaWgabaGaeGOmaidaaaaa@3906@ Channel variation v
σ p i n 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFdpWCdaqhaaWcbaGaemiCaaNaemyAaKMaemOBa4gabaGaeGOmaidaaaaa@33BE@ Spot pin variation v
σ X 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFdpWCdaqhaaWcbaGaemiwaGfabaGaeGOmaidaaaaa@30CE@ 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