Table 1

The number of shared differentially expressed genes found by the different methods for the Bottomly data set
ShrinkSeq DESeq edgeR NBPSeq TSPM voom vst baySeq EBSeq SAMseq
ShrinkSeq 3259 583 1125 985 1075 971 1049 192 803 1821
DESeq 583 598 598 567 588 589 587 191 523 592
edgeR 1125 598 1160 877 886 942 1013 194 753 1099
NBPSeq 985 567 877 1082 695 753 797 194 612 924
TSPM 1075 588 886 695 1161 891 907 191 794 1014
voom 971 589 942 753 891 1009 971 194 752 991
vst 1049 587 1013 797 907 971 1095 194 752 1061
baySeq 192 191 194 194 191 194 194 195 175 194
EBSeq 803 523 753 612 794 752 752 175 819 801
SAMseq 1821 592 1099 924 1014 991 1061 194 801 1860

The table contains the number of differentially expressed genes that are shared between each pair of methods, for the Bottomly data set (compare to Figure 5). The numbers on the diagonal, indicating the number of differentially expressed genes found by the respective methods, are highlighted in bold.

Soneson and Delorenzi

Soneson and Delorenzi BMC Bioinformatics 2013 14:91   doi:10.1186/1471-2105-14-91

Open Data