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We compared the accuracy of microarray measurements obtained with oligonucleotide arrays (Gene Chip, Affymetrix) with a laboratory-developed c DNA array by assaying test RNA samples from an experiment using a paradigm known to regulate many genes measured on both arrays.
We selected 47 genes represented on both arrays, including both known regulated and unregulated transcripts, and established reference relative expression measurements for these genes in the test RNA samples using quantitative reverse transcriptase real-time PCR (QRTPCR) assays.
The bias observed with c DNA arrays was predictable for fold-changes We describe detailed protocols and results with an integrated platform for studying relative transcript expression, including microarray design and fabrication, analysis and calibration algorithms, and high throughput quantitative real-time PCR.
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