ROC curves are plotted for DFI (black), EdgeR (red), DESeq (green), Cuffdiff (purple), and t-test (blue) methods based on qRT-PCR validated genes. (A) Comparison of DFI and p-values reported by EdgeR, DESeq, Cuffdiff and t-test shows that DFI is more accurate than p-values reported by the others. (B) Comparison of DFI and fold changes with p < 0.01 reported by EdgeR, DESeq and Cuffdiff shows that DFI is comparable to the combination of fold change and p-value criteria of the others. Since fold changes for Cuffdiff and t-test were both RPKM based they resulted in same values. Therefore, t-test is not plotted. Also, genes with less than 10 reads in both samples are not considered in this evaluation.
Ozer et al. BMC Genomics 2012 13(Suppl 8):S11 doi:10.1186/1471-2164-13-S8-S11