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In all of the special cases, an informative warning is output in Flow log. 

Since there is limitation in DESeq2(R), we recommend to use DESeq2 task all the time.

Fold change shrinkage in DESeq2

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.

Since there is limitation in DESeq2(R), we recommend to use DESeq2 task all the time.

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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