Flow chart of the method followed to analyze FFPE-FF sample pairs.

<p>70 FFPE and FF measurements (28 FFPE-FF pairs + 14 duplicate hybridizations) were used to establish a sample-quality threshold. A threshold of 2,208 was chosen and 7 FFPE samples (6x of the duplicates and 1x of the single hybridizations) with a median below this threshold were considered of poor quality and were excluded. Because the analysis is based on FFPE-FF pairs, 7 FF pairs matching the 7 FFPE samples with low median of the reference genes were excluded from the analysis. In addition, to exclude bias in the unsupervised analysis to be performed later, the two samples that remained from the duplicate hybridizations were excluded from the analysis. The duplicate samples were selected based on their median reference gene values; duplicate samples with the lowest median reference gene values were excluded from the analysis. Due to the duplicate hybridizations which did pass the exclusion criteria, only 1 sample pair was lost to the analysis because there was no FFPE data available. The other 25 tumors and 2 cell lines had all FFPE and FF data available for further analyses In total, 54 FFPE-FF measurements (27 FFPE-FF sample pairs) were used to develop the ruler based on the reliably measured probes.