False positive rates and sensitivity of differential expression (DE) with sequencing depth and number of replicate samples. Differentially expressed genes in GM12892 vs MCF-7 cell lines were divided into four count quartiles and false positive rate and sensitivity were measured by decreasing sequence counts and changing the number of replicate samples. Points and bars are average and standard deviation, respectively, from five random samples of reads from each library; see Materials and methods for details. (a) Number of false positives defined as the number of DE detected genes in GM12892 vs MCF-7 that were only identified by the specific method. (b) Sensitivity rates defined as the fraction of true set genes. Note that PoissonSeq's maximum sensitivity is below 1 since it was not included in the definition of the true set. See Figures S9 to S15 in Additional file 1 for similar plots for DE between other cell lines and technical replicates. DE, differential expression; FP, false positive.