Probe filtering step | Chromosome | n probes on 450k | n probes filtered (full cohort) | n probes filtered (sex-stratified) | Full cohort versus sex-stratified p-value* | Comment |
---|---|---|---|---|---|---|
Detection p-value | Auto | 473.864 | 4979 | 4979 | < < 0.00001 | Sex-stratify |
X | 11.232 | 143 | 143 | |||
Y | 416 | 359 | 3 | |||
Bead count | Auto | 473.864 | 4805 | 4805 | 0.76 | Do not stratify |
X | 11.232 | 94 | 94 | |||
Y | 416 | 3 | 1 | |||
Non-variable | Auto | 473.864 | 154.976 | 154.976 | 0.0005 | Sex-stratify |
X | 11.232 | 725 | 725 | |||
Y | 416 | 0 | 79 |