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For instance, the label 032-can-bk-bt-po corresponds to the cancerous, bulk tissue breast library whose number was 32 and was created by the laboratory labeled po. There are very few clusters: a brain cancer cell line cluster, a prostate cluster, a pancreas cluster, a mixed cluster containing brain and vascular tissue, and a breast cancer cell line cluster. Each of these clusters contains only 3 to 5 libraries, all of which are of a single type of tissue (with the exception of the cluster containing both brain and vascular tissue).

4. Result of OPTICS on the subspace selected by the Wilcoxon test including error removal, normalization, but NO missing tag imputation. ACM Transactions on Information Systems, Vol. 23, No. 1, January 2005. A Methodology for Analyzing SAGE Libraries for Cancer Profiling • 51 Fig. 5. Result of OPTICS on the subspace selected by the Wilcoxon test including error removal, normalization, and missing tag imputation. ACM Transactions on Information Systems, Vol. 23, No. 1, January 2005. 52 • J. Sander et al.

2000]: First, the SAGE method is highly prone to sequencing error, which creates a large amount of noise and obscures the clustering structure. Second, the libraries differ largely in terms of total number of tag copies due to differences in the depth to which individual SAGE libraries were sampled. Third, some of the SAGE libraries have been subjected to very limited sequencing, having 0 values for most of the tags. The fourth issue is that the “raw” data is extremely high dimensional. For our cluster analysis, each tag corresponds to a dimension.

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ACM transactions on information systems (January) by Association for Computing Machinery


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