Partek^® Flow^® provides DESeq2 method for differential expression detection, the implementation details of this algorithm can be found at: 

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 http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#the-deseq2-model

DESeq2 task can be invoked from the data node generated from quantification task, it contains raw read count values of each feature in each sample. Normalized counts is not appropriate to perform DESeq2 since DESeq2 model internally corrects for library size.

 If the value of the raw count has decimal point, the value will be rounded to integer be fore DESeq2 is performed.

DESeq2 dialog

DESeq2 dialog is very similar to ANOVA dialog, both categorical and numeric attributes can be added into the model. Interaction terms can also be added to the model, however, in order to perform contrast of the interaction term, a new attribute that combines the factors of interest should be added, and the contrast can be performed on the new combined attribute ( http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions)