The labeled nucleic acids are then hybridized to the microarray at 42-50 • C with 40-50% formamide (He et al., , 2010a Lu et al., 2012a) . Hybridization specificity can be adjusted by varying the temperature or the formamide concentration (the effective hybridization temperature increases by 0.6 • C for every 1% of formamide). Hybridized slides are then scanned and analyzed by quantifying the pixel density (intensity) of each spot using image analysis software. Commercial manufacturers often have their own analysis software or other microarray analysis software can be used, such as GenePix Pro (Molecular Devices, Sunnyvale, CA, USA), GeneSpotter (MicroDiscovery, San Diego, CA, USA), or ImaGene (BioDiscovery, El Segundo, CA, USA). For GeoChip data, there is a data analysis pipeline 2 for rapid preprocessing and data analysis. Poor and low quality spots and outliers, based on Grubbs' test of outliers (Grubbs, 1969) , are removed and then the signal intensities of all spots are normalized. Positive spots can be determined using signal-to-noise ratio [SNR = (signal mean − background mean)/background standard deviation], signal-to-both-standard-deviations ratio [SSDR = (signal mean − background mean)/(signal standard deviation − background standard deviation)] (He and Zhou, 2008) , or signalto-background ratio (SBR = signal mean/background mean) (Loy et al., 2002) .