A package that assesses RNA quality of Affymetrix expression data. The AffyRNADegradation package extends the Bioconductor package affy and integrates well in a typical microarray analysis workflow. All calculations are performed directly on the AffyBatch object and carried out separately for each particular microarray hybridization in a single-chip approach. Our approach corrects the 3′/5′-bias on the level of raw probe intensities, which can afterward be processed with any method. The runtime is about 2 min and 3 min per sample for index and distance based corrections, respectively. Because each chip is processed independently, arbitrarily large data sets can be processed.