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Pre-hybridization of microarray slides was previously described [24].
data of four microarray slides was used.
The most common cancer type in these tissue microarray slides was endometrial adenocarcinoma.
Quantile-quantile normalisation within and between microarray slides was implemented using the Limma Package of Bioconductor [ 105].
Microarray hybridization of samples and references to the ChillPeach microarray slides was performed manually using Telechem Hybridization Chambers (Corning), following the manufacturer's instructions.
The extraction of data from the TIFF files, generated through scanning the microarray slides, was performed using the Agilent Feature Extraction (FE Softwaree version 9.5.3.1 (Agilent Technologies).
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The microarray slides were custom-designed and contained 101,720, 60 mer probes.
The microarray slides were scanned using ScanArray Express.
Microarray slides were scanned immediately using an Agilent microarray scanner.
Microarray slides were hybridized and processed as described previously [42].
Microarray slides were manufactured by ArrayIt (Sunnyvale, CA).
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