dear BioC, could you suggest me a tool to RNAseq data upon differential expression analysis? as far as these data are not linear I am not sure if standard log2ratio and heat map are suitable. Claudio Isella claudio.isella at gmail.com

If you want something that you can plot in a heatmap, you might try using DESeq2, which squeezes the log fold changes of low-abundance genes toward zero so that your heatmap is not dominated by small fluctuations in low-abundance genes. On Mon Nov 25 14:22:02 2013, Claudio Isella wrote: > dear BioC, > > could you suggest me a tool to RNAseq data upon differential expression analysis? > as far as these data are not linear I am not sure if standard log2ratio and heat map are suitable. > > > > Claudio Isella > claudio.isella at gmail.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor