Table 1.

Number of bimodally expressed genes

Sample	Modela	Line effectb	Bimodalc
NC	Raw data	297	206
	Mixed model normalization	192	324
	Loess normalization	470	304
	Both mixed and loess	188	162
CA	Raw data	285	243
	Mixed model normalization	119	409
	Loess normalization	406	319
	Both mixed and loess	114	131
Common to both CA and NC		204	69d

^a'Raw data' refers to analysis directly on the log transformed raw fluorescence intensity measures, without normalization to remove array effects. 'Mixed model' refers to gene-specific models after mixed model normalization (as described in Materials and methods). 'Loess normalization' refers to analysis after loess treatment of the arrays. Note that loess increases the number of genes with significant line effects, but it reduces the number with apparent bimodality. ^bThe number of genes exhibiting greater line variation than the residual when treating the line effect as a random factor. ^cThe number of genes for which the mixture modeling indicates a greater likelihood that the distribution of transcript abundance across lines has two or more modes. ^dThe total number of genes with bimodal expression in both populations, either from the mixed (48 genes), loess (33 genes), or both modes of analysis (12 genes). CA, California, NC, North Carolina.