Clustering of mRNAseq gene expression: consensus NMF
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016  |  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 mRNAseq gene expression: consensus NMF. Broad Institute of MIT and Harvard. doi:10.7908/C1MP52P7
- Overview
+ Introduction
- Summary

The most robust consensus NMF clustering of 290 samples using the 1500 most variable genes was identified for k = 5 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
+ Gene expression patterns of molecular subtypes
+ Silhouette widths, Cophenetic Correlation Coefficients and Consensus matrix
+ Samples assignment with silhouette width
+ Marker genes of each subtype
+ Methods & Data