Table 1

Number of bimodally expressed genes

Sample

Model^a

Line effect^b

Bimodal^c

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

69^d

^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.

Hsieh et al. Genome Biology 2007 8:R98   doi:10.1186/gb-2007-8-6-r98