The microarray data for each gene were fitted to a simple control versus treatment linear model at each time point/comparison, and statistics were generated using the lmFit and eBayes functions [ 42] of the LIMMA package.
LIMMA was performed using the lmFit and eBayes functions from the limma R package for the R Statistical Language with default parameters.
After the 'SC-2D+quantile' normalization, the six comparisons (or effects) of interest were estimated by the least squares method using the lmFit Limma function [57] The correlation between the spots of the three dyes within each gel was first estimated using the Limma dupcor function [58].
Analysis were performed with the limma package [ 32], using the lmFit function.
A linear model was fitted for each gene in a given series of arrays by using the lmFit function.
Afterwards, the linear model was fitted using the lmFit function, which fully models the systematic part of the data.
Briefly, data were normalized with the Lowess method, and differential expression analyses were carried out using the lmFit function and the Bayes moderated t test using the R package LIMMA [ 62] from the Bioconductor project.
In most cases, all replication is biological, so we generate fits using the lmfit function in limma; for the JZ12 (GSE37068) data set, technical replicates were fit using the duplicateCorrelation function in limma.
We, therefore, fit a linear model with date and experimental conditions summarized in Table 1 using the lmFit function in the R Bioconductor package limma (Linear Models for Microarray Data; [ 36]).
Robust multichip average (RMA) [ 107] and print tip lowess normalization [ 108, 109] were performed on the data before differential expression analyses were performed using the lmFit function in LIMMA.
Further, we estimated the fold change and standard errors by fitting a linear model (using the lmFit function) for each gene given the groups of arrays and then compute a moderated t-statistics of differential expression by applying empirical Bayes at a level of 0.05.
