Experimental design

Thirty-five RCC samples (13 ccRCC, 13 pRCC, and 9 chRCC) were labeled individually with Cy3. A Cy5-labeled sample pool of 28 tumor RNA samples (15 ccRCC, 8 pRCC, and 5 chRCC) was used as a common reference for all hybridizations. Both Cy3- and Cy5-labeled samples were hybridized competitively against the cDNA probes on the microarrays. The pixel intensities for each spot were quantified, and data were normalized as described (19). The generalized log ratios were used for tumor classification.

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