Principal component analysis and association test of global gene expression with seed development
The normalized, log2-transformed gene expression data were used for principal component analysis (PCA) using the R prcomp function [83]. For this analysis, expression values of the three replicates for each seed development stage were not combined in order to assess the reproducibility of biological replication. Global testing of the transcriptome with a particular variable (e.g., seed development stage) was carried out using the Globaltest package [51]. This package tests the overall gene expression in group(s) of genes for significant association with a given variable. The test gives one P-value for the whole group instead of one P-value for each gene to avoid the issue of multiple testing corrections.