Apart from general considerations regarding the normalization of data in biology, special considerations apply to the normalization of quantitative real-time polymerase chain reaction (PCR) data [ 4].
Mathematical best fits were applied to the curves after normalization using the Gaussian function (Fig. 2).
Lowess (locally weighted scatter plot smoothing) normalization was applied to the data to normalize the spot intensity from various replicates.
RNA was hybridized to Affymetrix's Mouse Expression Set 430 A; chips were scanned with the GeneChip Scanner 3000 and VSN normalization was applied to the gene expression data for normalization.
Note that the normalization applied to the ratios in order to correct for microarray block and dye intensity-dependent effects constrains the global mean to exactly one.
However, the number of samples analyzed here, as well the normalization applied to the NMR data, are distinct from the previous study.
DR has become almost a standard practice just following the pre-processing steps typically applied to the experimental measurements (mining, normalization, etc).
Several preprocessing steps have been applied to the data, including temporal normalization to give the data equal weight and ensemble mean subtraction to remove first-order nonstationarity [27].
To identify differentially expressed genes, a generalized linear model was applied to the data after DEseq normalization (DESeq's GLM method using the gene data set).
