Table 1. Normalization of three ChIP-chip data sets.

Experiment		StandardNormalization	Invariantnormalization	HMM-assistednormalization
H3K27me3	Enriched (M>1.5)	27004	24110	45317
	M<−1.5	5441	6687	650
E(z)	Enriched (M>1.5)	3927	4057	4440
	M<−1.5	0	0	0
PolII	Enriched (M>1.5)	14435	20392	22395
	M<−1.5	3	0	0

The number of probes identified as being enriched (i.e. having an M-value>1.5) and the number of probes with M-values below −1.5 for the H3K27me3, E(z) and PolII experiments. Arguably, the number of false positives in analyses using the HMM and invariant normalizations can be estimated as the number of probes below −1.5.