Clustering of RPPA data: consensus NMF
Stomach and Esophageal carcinoma (Primary solid tumor)
28 January 2016
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analyses__2016_01_28
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/C1NG4Q3B
Overview
Introduction
Summary
The most robust consensus NMF clustering of 483 samples using the 196 most variable proteins was identified for k = 4 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
Copyright © 2016
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.