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Here, we have focused on CN estimates from different labs and technologies, but the proposed model and method may also be applied for normalizing estimates from different chip types of the same technology, e.g. when combining data from the two chip types part of the Affymetrix 500K chip set.
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Print-tip loess is applied for Within Array normalization and quantile normalization is used for Between Arrays to normalize between chips.
ComBat (Johnson et al, 2007), a high precision and accurate technique for removing batch effect while conserving meaningful variation (Chen et al, 2011), was applied for batch adjustment on the compiled, normalized data.
StepOne software version 2.2.2 (Life Technologies Applied Biosystems) was applied for comparative analysis, and the quantification was normalized with 18 S gene.
Briefly, probe logarithmic intensity error estimation (PLIER) was used to enhance probe signals by summarization; perfect match GC composition-based background correction (PM GCBG) was applied for background correction and global median to normalize the signals.
Lysates, normalized by protein level, were applied for the ELISA-based phospho-Akt assay.
It should be noted that in the following testing strategies Normalized Discounted Cumulative Gain (NDCG) was applied for the quantitatively comparison of different VS methods.
StepOne software version 2.2.2 (Life Technologies Applied Biosystems) was applied for comparative analysis, and the relative expression level was normalized with GAPDH gene expression.
The comparative ΔΔ Ct method was applied for quantitation of PCR product and Plp1 mRNA expression was normalized against Ppia mRNA.
The ability to work in the natural units of analyte concentration, as opposed to transformed units that might be applied in an attempt to normalize datasets for a parametric analysis, also simplifies interpretation of results.
Quantile normalization was applied to normalize between arrays [ 37].
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