Differential Expression Analysis of Long Noncoding RNAs.

Long noncoding RNA (lncRNA) expression data have been increasingly used in identifying diagnostic and prognostic biomarkers in clinical studies. Low-expression genes are commonly observed in lncRNA and need to be effectively accommodated in differential expression analysis. In this chapter, we describe a protocol based on existing R packages for lncRNA differential expression analysis, including lncDIFF, ShrinkBayes, DESeq2, edgeR, and zinbwave, and provide an example application in a cancer study. In order to establish guidelines for proper application of these packages, we also compare these tools based on the implemented core algorithms and statistical models. We hope that this chapter will provide readers with a practical guide on the analysis choices in lncRNA differential expression analysis.