Analysis Overview for PANCANCER cohort with 18 disease types

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

This is the analysis overview for Firehose run "21 December 2012".

Summary

Note: These results are offered to the community as an additional reference point, enabling a wide range of cancer biologists, clinical investigators, and genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research. While every effort is made to ensure that Firehose input data and algorithms are of the highest possible quality, these analyses have not been reviewed by domain experts.

Results

Clustering Analyses

Clustering of miR expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 568 samples and 150 miRs identified 3 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.
Clustering of miR expression: consensus hierarchical
View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 568 samples and 150 miRs identified 6 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.

Other Analyses

The boxplot mRNA array based expression data
View Report

Methods & Data

Input

Run Prefix = analyses__2012_12_21
Summary Report Date = Fri Jan 25 12:02:40 2013
Protection = FALSE

Made with Nozzle