HOXA1 knockdown in lung fibroblasts
The analysis in this section assesses the current version of Cuffdiff using the data from Trapnell and Hendrickson et al. In that study, RNA-Seq results with Cuffdiff was compared against DESeq, edgeR, and other popular tools. The RNA-Seq results were also compared against microarrays.
In the above plot, log fold changes obtained by RNA-Seq (using Cuffdiff 2) are compared against those obtained with Agilent expression microarrays.
Each point is a gene, and points are colored by whether they are called as significantly DE by Cuffdiff only (red), microarrays only (green), both (blue) or neither (violet).
The venn diagram above illustrates concordance between genes reported as significantly DE by Cuffdiff and microarrays.
The venn diagram above illustrates concordance between genes reported as significantly DE by the current release of Cuffdiff, version 2.0.2 (used in Trapnell and Hendrickson et al), and DESeq.