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Series GSE55763 Query DataSets for GSE55763
Status Public on Jan 22, 2015
Title A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence.
Overall design Bisulfite-converted DNA for 2,664 human samples and 36 technical replicates were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2.
Contributor(s) Lehne B, Drong A, Loh M, Zhang W, Scott WR, Tan ST, Afzal U, Scott J, Jarvelin MR, Elliott P, McCarthy MI, Kooner JS, Chambers JC
Citation(s) 25853392, 28002404
Submission date Mar 10, 2014
Last update date Jul 06, 2022
Contact name Benjamin Lehne
Organization name Imperial College London
Department Epidemiology and Biostatistics
Street address Medicine, Norfolk Place, St Mary's Campus
City London
ZIP/Postal code W2 1PG
Country United Kingdom
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (2711)
GSM1343050 Peripheral blood, 7786915023_R02C02
GSM1343051 Peripheral blood, 7786915135_R04C02
GSM1343052 Peripheral blood, 7471147149_R06C01
Reanalyzed by GSE207605
BioProject PRJNA240908

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE55763_RAW.tar 183.1 Mb (http)(custom) TAR
GSE55763_normalized_betas.txt.gz 9.7 Gb (ftp)(http) TXT
GSE55763_unmethylated_methylated_signal_intensities.txt.gz 5.7 Gb (ftp)(http) TXT
Processed data are available on Series record

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