README for TCGA archive jhu-usc.edu_LAML.HumanMethylation27.1.0.0
The data archive contains The Cancer Genome Atlas (TCGA) analysis of DNA methylation profilings using the IIllumina Infinium Human DNA Methylation27 platform. The Infinium platform analyzes up to 27,578 CpG dinucleotides spanning the entire set of 14,495 Consensus Coding DNA Sequence (CCDS) genes. DNA samples were received, bisulfite converted and the methylation profiling was evaluated using IIllumina Infinium Human DNA Methylation27 technology.
This archive contains Infinium-based DNA methylation data for 188 Acute Myeloid Leukemia (AML) samples from Batch 25.
The data levels and the files contained in each data level package are described below:
LEVEL 3: Level 3 data contain beta value calculations, gene IDs and genomic coordinates for each probe on the array. In addition, we have masked data for probes that contain known single nucleotide polymorphisms (SNPs) after comparison to the dbSNP database (Build 130). In addition, we have masked data for probes that contain repetitive element DNA sequences that cover the targeted CpG dinucleotide in each 50 bp probe sequence.We have also masked probes that are not uniquely aligned to the human genome (build 36) at 20 nucleotides at the 3' terminus of the probe sequence, as well as those that span known regions of insertions and deletions (indwells) in the human genome. Data points from probes containing SNPs, repetitive elements, other non-unique sequences and/or indwells are masked with an NA descriptor.
10-Jun-10