Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

Table 3 Summary of the probes which are removed or kept for further analysis

	Infinium I	Infinium II	Total kept
Total number of probes on array	135,476	350,036	-
Probes which map to multiple genomic locations	1,581	3,728	0
Probes containing known repeat regions	2,845	13,673	0
Probes containing known INDELs	1,885	4,101	5,986
Probes containing SNP and interrogated CpG	9,568	42,800	0
Probes containing 1 SNP in the body	26,700	72,315	77,545*
Probes containing > =2 SNPs in the body	20,043	34,330	34,675*
Probes affected by unknown factors	1,394	13,840	0
Probes affected by multiple factors	16,857	49,580	4,047*
Total number of ‘rescued probes’	7,367	114,886	122,253
Total number of high-quality probes	52,817	119,770	172,587
Total number of probes kept for further analysis	60,184	234,656	294,840

*Some of these probes were rescued due to being bisulfite OK.
The probe counts depicted in this table are those which are unique to each category. Any probes which have are affected by multiple factors appear in the ‘Probes affected by multiple factors’ category.

ISSN: 1471-2164