bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
Scan protocol
Arrays were imaged using standard recommended Illumina scanner protocol
Description
A949
Data processing
The methylation value was set to null for probes with a detection p-value < 0.01. A strict filtering step was performed to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested. We only retained those probes that had either a perfect match, or had 1 or 2 mismatches in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately.
