An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

BMC Genomics

Table 1 Number of validated estrogen receptor α targets found significantly enriched in the estrogen receptor α ChIP-on-chip dataset (dataset #1).

	Number of ER-a targets found (out of 33)
Normalization approach	Enrichment p-value < 0.05	< 0.10	< 0.20	< 0.50
VSN	7	8	11	23
LOWESS	6	7	10	25
Quantile	8	9	12	25
T-quantile	9	10	14	24
Tukey's biweight scaling	7	8	11	23
Peng's method	5	5	9	23

Table 1 contains for each of the tested normalization approaches the number of validated estrogen receptor α targets [25] found significantly enriched in the estrogen receptor α ChIP-on-chip dataset (dataset #1). Results for four enrichment p-value cut-offs are given (0.05, 0.10, 0.20 and 0.50).

ISSN: 1471-2164