Principal component analysis and volcano plot of differentially abundant transcripts. (A) Principal component analysis revealed the greatest variability in RNA-Seq data was due to the age of the donor. (B) A set of differentially expressed genes between young and old cartilage was discovered. Using the common dispersion in edgeR , 396 differentially expressed genes were identified with P < 0.05 (red). To enable expression of all genes to be visualised simultaneously, a smear plot was produced. The smear at the left-most edge allows visualisation of genes with zero counts in one of the groups. This was undertaken as if the total counts in one group are zero, the log fold-change is technically infinite, and the log concentration is negative infinity.
Peffers et al. Arthritis Research & Therapy 2013 15:R98 doi:10.1186/ar4278