Additional file 1.

Contains supplementary figures referred to in the text. Here, we also evaluate the effect of selecting different values for the parameters of edgeR and DESeq and evaluate two additional transformation-based methods, and we evaluate the effect of simulating data with different dispersion parameter in the two compared conditions. We also present some comparisons based on data sets with 3 samples per condition. The file also contains information regarding the estimation of the mean and dispersion parameters from real data, and an additional analysis of two real RNA-seq data sets. Finally, it contains sample R code to run the differential expression analysis and estimates of the computational time requirements for the different methods.

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