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The DESeq2(R) task can be invoked from data nodes generated by quantification tasks that contains raw read count values for each feature in each sample (Gene counts, Transcript counts, microRNA counts, etc.). DESeq2(R) cannot be run on a normalized counts data node because DESeqDESeq2(2R) internally corrects for library size and implements a low expression filter.

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In R, shrinkage of log2 fold changes is a separate step performed by lfcShrink() function. In Flow, that functionality is absent in DESeq(R) but present in DESeq2 task. The latter implements the shrinkage method corresponding to “ashr” option in lfcShrink(). The default shrinkage option in lfcShrink is “apeglm”, but the default method is unable produce results for some comparisons whereas “ashr” has no restrictions. The fold change shrinkage results are produced in “Shrunken Log2(Ratio)” and “s-value” columns in DESeq2 task project report.

References

Love MI, Huber W, and Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 2014;15(12): 550.

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