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In fact, we and others have previously proposed median gene centering to minimize technical bias and allow the correct identification of the PAM50 intrinsic subtypes when appropriate representation of ER−, ER+, and HER2+ samples is available [ 31, 32].
We applied experimental designs to minimize technical bias, described in Methods, and plots of the genotyping measurements (P1[B]/P1[A] ratio, mean LRR, and mean BAF) do not provide any evidence for bias between cases and controls (Supp. Figs. S1 and S6).
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An effective normalization technique should minimize technical and experimental bias without introducing noise.
To minimize technical CNV detection biases we: (1) used data only from the same platform (when available), (2) used data from the highest resolution genome-wide survey published on each species queried and (3) required that the study was non biased to any particular genomic region.
Then, attempts were made to minimize technical variables as a source of bias in reporting this study.
This helped minimize technical noise associated with oligodeoxyribonucleotides labeling efficiency.
This selection procedure was performed twice to minimize technical errors and false positives.
Reciprocal dye swap replicate hybridizations were performed to minimize technical noise.
We applied stringent quality control and filtering procedures to minimize technical variation.
All samples were, however, stored and processed in the same manner to minimize any technical bias into the comparative analysis.
Microarrays were processed by one person at the Laboratory of Molecular Technology, National Cancer Institute (NIH, Frederick, MD), following standard operating protocol to minimize non-biologic technical bias.
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