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GMQN

Name	GMQN
Type	Health and Disease Detection
Version	v1.0
Developers	Zhuang Xiong, Mengwei Li, Yingke Ma, Rujiao Li, Yiming Bao
Description	The Illumina HumanMethylation BeadChip is one of the most cost-effective methods to quantify DNA methylation levels at single-base resolution across the human genome, which makes it a routine platform for epigenome-wide association studies. It has accumulated tens of thousands of DNA methylation array samples in public databases, providing great support for data integration and further analysis. However, the majority of public DNA methylation data are deposited as processed data without background probes which are widely used in data normalization. Here, we present Gaussian mixture quantile normalization (GMQN), a reference based method for correcting batch effects as well as probe bias in the HumanMethylation BeadChip. To achieve this process, GMQN standardizes the data in three steps. The first step is the establishment of a reference distribution. To address the issue of rapid growth in public data, GMQN adopts a standardization method based on the reference distribution. The average signal strength of each probe in the reference dataset is calculated across samples, and Gaussian mixture distributions are fitted to the signal strengths of probes on the red and green channels separately. The second step is inter-chip normalization. Inter-chip normalization is performed separately on the red and green channels of probes. First, the signal strengths of a certain type of probe in the input are fitted to a Gaussian mixture distribution, and fitting parameters are obtained. Then, the input signals are mapped to the reference signals to remove batch effects and other biases. The third step is intra-chip normalization, primarily aimed at removing biases of a certain type of probe. In the second step, we obtain standardized signal strengths for a certain type of probe. Using the signal strengths of this type of probe as the reference, we apply BMIQ or SWAN for normalizing the signal strengths of the other type of probes. We have made some adjustments to BMIQ and SWAN to improve their speed and effectiveness.
Downlaod	https://ngdc.cncb.ac.cn/biocode/tools/BT007369
Article	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8777061/
Cite Count	9
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