Partek^® Flow^® offers Partek Flow offers the DESeq2 method for differential expression detection. There are two options DESeq2(R) and DESeq 2.

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Categorical and numeric attributes, as well as interaction terms can be added to the DESeq2 model. The DESeq2 configuration dialog for adding attributes and interactions to the model is very similar to the ANOVA configuration dialog. However, DESeq2(R) has two important limitations not shared by GSA or ANOVA/LIMMA-trend/LIMMA-voom.

First, interaction terms cannot be added to contrasts in DESeq2(R). In order to perform contrasts of an interaction term in DESeq2(R), a new attribute that combines the factors of interest must be added and the contrast performed on the new combined attribute. This limitation of DESeq2(R) is detailed in the official DESeq2 documentation page. To perform contrasts of interaction terms without creating new combined attributes, please use either DESeq2, GSA, or ANOVA/LIMMA-trend/LIMMA-voom method.

Second, DESeq2(R) only allows two subgroups to be compared in each contrast. To analyze multiple subgroups, please use either DESeq2, GSA, or ANOVA method. 

In DESeq2 advanced options configure dialog, there is reference selection option:

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The report produced by DESeq2 is similar to the ANOVA report; each row is a feature and columns include p-value, FDR p-value, and fold change in linear scale for each contrast. However DESeq2(R) report doesn't have LSMeans information on the compared groups.

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