To evaluate the effect of technical repetition on gene expression measurements, we repeated the laboratory protocol at 6 different steps. Information was used to select probesets with a high technical reproducibility for the development of gene signatures.
Overall design
20 breast cancer samples were profiled on Affymetrix U133A microarrays. The samples were chopped in pieces, mixed and 80% were used to repeat the laboratory protocol at five different levels: RNA extraction, cDNA synthesis, cRNA synthesis and re-scan of the same chip. The remaining 20% of the sample mix were used to repeat all steps, resulting in a total of six technical replicates.
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