We’re beginning to explore software for the analysis of miRNASeq data and are interested in performing differential expression analysis using a dichotomous trait (cases vs controls) as well as a continuous trait.  While I know that the former can be implemented in DESeq2, I’m not sure whether the latter can; can you comment on this?  If continuous traits can be analyzed, can you provide an example on how to analyze this?  In reviewing the vignette, this is not clear to me.  

Thanks in advance!

hi Marcus,

Take a look at the Frequently Asked Questions at the end of the vignette:

vignette("DESeq2")

...assuming you are using DESeq2 version >= 1.4 (released Apr 2014). If you are using version 1.2 (Oct 2013) or earlier, you should try first upgrade to the latest version of Bioconductor:

http://bioconductor.org/install/