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Microarray normalization procedures were performed as described for the cell line experiment.
They note that microarray normalization procedures mitigate such phenomenon, but are unable to completely negate them.
Subsequently, we applied this method to evaluate various microarray normalization procedures [ 41].
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The aCGH signal intensities were normalized using a two-channel microarray normalization procedure.
In the data analysis we combine a new microarray normalization procedure with a conglomerate measure of significant differential gene expression.
We think that the microarray normalization procedure removes the skew, which leads to inaccurate normalization, and consequently inaccuracy in identification of differentially expressed genes.
The detailed protocol for microarray hybridization and normalization procedures were described by Horak et al [65] and are available upon request.
Since the normalization procedure greatly changes the microarray data, different normalization procedures may lead to very different clustering results.
Gene expression was measured on Illumina HT-12 microarrays with two different normalization procedures to control technical and biological covariates.
Microarray scanning, feature extraction and normalization procedures were performed as described for the cell line experiment.
RLM contributed to experimental design, undertook cDNA library construction, target labeling and microarray hybridizations, spot editing and normalization procedures.
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