This is the analysis overview for Firehose run "25 May 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 57 tumor samples used in this analysis: 21 significant arm-level results, 15 significant focal amplifications, and 24 significant focal deletions were found. -
Clustering Analyses
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Clustering of miRseq expression: consensus NMF
View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 28 samples and 150 miRs identified 2 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 miRseq expression: consensus hierarchical
View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 28 samples and 150 miRs identified 2 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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Correlation between molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 2 different clustering approaches and 2 clinical features across 24 patients, no significant finding detected with P value < 0.05.
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Firehose Directory = /local/cga-fh/tcga-gdac
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Run Prefix = analyses__2012_05_25
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Summary Report Date = Sat Jun 16 13:04:58 2012
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Protection = FALSE