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Table 1 Summary of the number of samples flagged by each of the 17 control metrics outlined in the BeadArray controls reporter software guide. n.a.—not available

From: Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO

Metric

Passed

Flagged

n.a.

Restoration

8326

0

1

Staining green

7885

10

432

Staining red

7764

14

549

Extension green

8324

3

0

Extension red

8326

1

0

Hybridization high/medium

8326

1

0

Hybridization medium/low

8327

0

0

Target removal 1

8327

0

0

Target removal 2

8327

0

0

Bisulfite conversion I green

8317

10

0

Bisulfite conversion I red

8208

119

0

Bisulfite conversion II

7950

377

0

Specificity I green

8323

4

0

Specificity I red

8279

48

0

Specificity II

8326

1

0

Non-polymorphic green

7677

558

92

Non-polymorphic red

7917

318

92

Any of the above

7387

940