Lung Adenocarcinoma: Clustering of Methylation: consensus NMF
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
- Overview
+ Introduction
- Summary

The 3655 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 181 samples and 3655 genes identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

- Results
+ Silhouette width of each sample in robust cluster
+ Gene methylation patterns of molecular subtype
+ Consensus and correlation matrix
+ Samples assignment with silhouette width
+ Marker genes of each subtype
+ Methods & Data