Skip to main content

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

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

  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
  1. *Some of these probes were rescued due to being bisulfite OK.
  2. 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.
\