Analysis of microarray data

Transcript profiling analysis was conducted using Affymetrix GeneChip® Wheat Genome Arrays (cat # 900558). The Affymetrix wheat genome array is composed by 61,127 probe sets that represent 55,052 transcripts distributed in all 42 chromosomes. Using robust multiarray average (RMA) method, each set of raw data was background corrected, log₂-transformed and normalized through the Affy package from Bioconductor (Gautier et al., 2004). The limma package was utilized to conduct empirical Bayes moderated t-test (Ritchie et al., 2015). P-values were adjusted to control the false discovery rate (FDR) using Storey and Tibshirani method (Storey and Tibshirani, 2003). Annotations from differentially expressed transcripts were blasted with the rice, Arabidopsis and Brachypodium genome. The microarray data was deposited in NCBI's Gene Expression Omnibus (Edgar et al., 2002) under the GEO series accession number {"type":"entrez-geo","attrs":{"text":"GSE84330","term_id":"84330","extlink":"1"}}GSE84330.