RNA Sequencing Data Analysis
STAR aligner was used (splice junction annotations based on GENCODE
version 27; www.gencodegenes.org) to map paired-end raw reads to human
genome build GRCh38. Based on GENCODE v27, mapped reads and gene
annotations were enumerated using featureCounts. edgeR bioconductor
package was used to compute log2 transformed counts per million mapped
reads (log2CPM) and log2 transformed reads per kilobase per million
mapped reads (log2RPKM). Removal of genes with the log2CPM
inter-quartile range (IQR) of which across all samples was less than 0.5
preceded analysis of differentially expressed genes. Pairwise
comparisons of differentially expressed genes between AR and non-AR was
performed using edgeR. P-values were corrected for multiple testing
using the Benjamini-Hochberg procedure (Benjamini, 2010) and false
discovery rate (FDR). Corrected p-values were presented with a
significance threshold of 0.05. Differentially expressed gene analysis
was carried out using edgeR with the eosinophil percentage as a
covariate. Default parameters were applied to run all software listed
above.