The data archive contains The Cancer Genome Atlas (TCGA) analysis of DNA methylation profilings using the Illumina Golden Gate Methylation Bead Array platform. DNA samples were received, bisulfite converted and the methylation profiling was evaluated using Illumina DNA Methylation Golden Gate technology.

This archive contains data on one DNA methylation bead array for 21 GBM tumor samples from Batch 7 and 6 GBM tumor samples from Batch 5.

The AVG_beta value represents the final methylation value for each locus, while the Cy3 and Cy5 measurements represent methylated and unmethylated DNA signal intensities for each hybridization. The Detection p-values (Detection PVAL) provide an indication of DNA methylation measurement quality for each locus.

Detection p-values are also included in the data package. Data points with a p-value > 0.05 cannot be significantly distinguished from background controls and are renamed "N.A" Samples with < 80% of the data points with detection p-value > 0.05 are removed from the data package. No samples in this data package were removed due to QC.

OMA002 refers to the second version of the Illumina GoldenGate DNA methylation Oligonucleotide pool for Methylation Assay (OMA), described by Illumina as DNA Methylation Cancer Panel I (CPI).

Data package includes full data information for each sample using background subtraction normalization method, i.e., AVG_beta value, cy3 measurement, cy5 measurement, and p-value.

April 25, 2008
