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Introduction: Normalization of high throughput array data reduces the background noise between samples. However, most normalization techniques will correct differences between paired samples after treatment similarly as background noise and remove valuable information. We developed a new normalization technique for analyzing methylation arrays data after demethylating treatment effects in paired samples.

Materials and methods: neuro-ectodermal tumor cell lines (18 NBL and 5 PNETs) were treated with methylation inhibitors and HDAC inhibitors. We used 30 nM Decitabine (DAC) for 72 hours and 25 nM Trichostatin A (TSA) for the last 48 hours of treatment. Samples before and after treatment were subjected to 244 K CpG island arrays (Agilent).

Results:

Conventional normalization: Normal Loess normalization and VSN two channel normalization were initially used and showed that the …