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Table 1 Pearson Coefficients between cores and corresponding tumor samples

From: Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors

Sample DU145 (LN2) Whole Tumor All Genes DU145 (LN2) Whole Tumor Outliers U251 (later) Whole Tumor All Genes U251 (later) Whole Tumor Outliers
Core 1 0.827 0.979 0.824 0.950
Average N = 6,785 genes N = 436 genes N = 6,880 genes N = 381 genes
Core 2 0.846 0.979 0.750 0.972
Average N = 6,883 genes N = 416 genes N = 6,786 genes N = 396 genes
Core 3 0.812 0.970 0.834 0.973
Average N = 6,772 genes N = 340 genes N = 6,840 genes N = 389 genes
  1. "All Genes" were extracted with the following parameters: Spots flagged as Bad/Not Found were excluded, and spots with target diameters outside of 50 μm and 300 μm were excluded. "Outliers" were extracted with the following parameters: Sgl/Bkg ratio >= 2, signal >= 1,000, override if either channel >= 2,500, target pixels 1 SD about Bkg >= 80%, target diameter btw 50 μm and 300 μm, genes required values in 100% of arrays, and ratio >= 2 in >= 2 arrays (applied symmetrically)