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Table 2 Number of probes indexed as failing during detection p-value, bead count, and non-variable probe checks

From: Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data

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

  1. Detection p-value indexes probes with a detection p > 0.01 in > 1% of samples, bead count refers to probes with a bead count of  < 3 in > 1% of samples, and non-variable refers to the number of probes with a range of DNAme beta values of  < 5% across samples
  2. *p-values from Fisher’s exact tests for categorical variables