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Fig. 2 | Clinical Epigenetics

Fig. 2

From: Improved filtering of DNA methylation microarray data by detection p values and its impact on downstream analyses

Fig. 2

Detecting what is not supposed to be there. Call rates of Y-chromosome probes among the 1442 female samples for three approaches to classifying detected probes. Probes are ordered on the x-axis by increasing call rate (order not identical between curves). Only six probes had a call rate <ā€‰2% when using the conventional cut-off of 0.01 with the background distribution estimated from negative control probes (NEG/0.01). For more stringent criteria (NSP/0.1 and NEG/1eāˆ’40), there is an almost clear-cut separation between undetected and detected probes including some cross-hybridizing to autosomal CpG sites

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