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.

plot of chunk unnamed-chunk-1

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).

plot of chunk array_venn

The venn diagram above illustrates concordance between genes reported as significantly DE by Cuffdiff and microarrays.

plot of chunk curr_vs_prev_vs_deseq_venn

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.