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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)
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BMC Cancer

ISSN: 1471-2407

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