Additional file 1.

Supplementary figures. All the supplementary figures referenced in the main text. 1 Hierarchical clustering of the SEQC libraries from sample A and B . . . . . . . . . . 3. 2 Hierarchical clustering of the ENCODE samples .................... 4. 3 Dunn clustering validity index............................... 5. 4 Normalized read counts .................................. 6. 5 ROC analysis of ERCC spike-in controls.........................7. 6 Null model p-values distribution without replicate samples . . . . . . . . . . . . . . . 8. 7 Evaluating monotonic correlation between signal-to-noise and p-values in genes expressed in only one condition ............................... 9. 8 Correlation of signal-to-noise ratio and DE p-values from SEQC data set . . . . . . . 10. 9 Methods performances with reduced sequencing depth and number of replicates for detecting DE between GM12892 and H1-hESC............... 11. 10 Methods performances with reduced sequencing depth and number of replicates for detecting DE between H1-hESC and MCF-7.................. 12. 11 Impact of sequencing depth and number of replicate samples on DE detection by DESeq using SEQC data.................................. 13. 12 Impact of sequencing depth and number of replicate samples on DE detection by edger using SEQC data.................................. 14. 13 Impact of sequencing depth and number of replicate samples on DE detection by limmaQN using SEQC data................................ 15. 14 Impact of sequencing depth and number of replicate samples on DE detection by limmaVoom using SEQC data............................. 16. 15 Impact of sequencing depth and number of replicate samples on DE detection by PoissonSeq using SEQC data ............................. 17. 16 Over-dispersion of the ENCODE dataset ........................ 18}.

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Rapaport et al. Genome Biology 2013 14:R95   doi:10.1186/gb-2013-14-9-r95