Clustering of RPPA data: consensus NMF
Liver Hepatocellular Carcinoma (Primary solid tumor)
14 July 2016  |  awg_lihc__2016_07_14
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Clustering of RPPA data: consensus NMF. Broad Institute of MIT and Harvard. doi:10.7908/C1SJ1K4X

Note: The original LIHC RPPA data used on 2016_01_28 was reported to be mislabelled Mesothelioma RPPA data. The affected analyses were patched on 10/13/2016, and contain this notice. For more details see our analysis release notes.

- Overview
+ Introduction
- Summary

The most robust consensus NMF clustering of 184 samples using the 219 most variable proteins was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 10 and uused the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

- Results
+ Protein expression patterns of molecular subtypes
+ Silhouette widths, Cophenetic Correlation Coefficients and Consensus matrix
+ Samples assignment with silhouette width
+ Marker proteins of each subtype
+ Methods & Data