Skip to main content

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 –