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  • All arrays were normalized using dChip software v1.3 [[pgen-0010008-b28]]. Model-based expression index was obtained by PM/MM difference algorithm in dChip. Gene filtering and hierarchical clustering analysis were also performed in dChip [[pgen-0010008-b29]]. To deal with variable degrees of quality in sample hybridization and resulting control parameters, such as absolute (%P) call and 5′/3′ ratios of housekeeping genes (GAPDH and actin), we subclassified the samples into three categories: superior, good, and satisfactory quality. For each gene, samples belonging to each category were separately computed for coefficient of variation (standard deviation/mean) for gene filtering and standardized (to achieve mean = 0 and SD = 1) for gene and sample clustering. Duplicated samples were combined prior to standardization.


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