Analysis Overview for Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

This is the analysis overview for Firehose run "16 January 2013".


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.

  • Sequence and Copy Number Analyses

    • Copy number analysis (GISTIC2)
      View Report | There were 18 tumor samples used in this analysis: 8 significant arm-level results, 1 significant focal amplifications, and 12 significant focal deletions were found.

  • Clustering Analyses

    • Clustering of Methylation: consensus NMF
      View Report | The 15446 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 17 samples and 15446 genes 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.

Methods & Data
  • Run Prefix = analyses__2013_01_16

  • Summary Report Date = Mon Feb 11 17:44:45 2013

  • Protection = FALSE