This is the analysis overview for Firehose run "21 December 2012".
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.
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Sequence and Copy Number Analyses
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Copy number analysis (GISTIC2)
View Report | There were 4688 tumor samples used in this analysis: 33 significant arm-level results, 40 significant focal amplifications, and 50 significant focal deletions were found. -
Clustering Analyses
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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
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The boxplot mRNA array based expression data
View Report
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Run Prefix = analyses__2012_12_21
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Summary Report Date = Fri Jan 25 12:02:32 2013
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Protection = FALSE