Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

Table 1 Numbers of differentially expressed genes between batches within a single experiment identified using ANOVA

Adjustment Method	Cincinnati	UC Davis	Common
None	48	527	3
t-test filter	0 (of 273)	42 (of 273)	0
EB: between experiment only	96	545	8
EB: within experiment only	0	4	0
EB: within and between experiment	0	0	0

Numbers are out of 54,675 probe sets unless otherwise specified. EB = empirical Bayes.

ISSN: 1471-2164