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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.

Troubleshooting

In addition to the issues addressed in Differential Analysis Troubleshooting, DESeq2 may generate missing values in the multiplicity adjustment columns (such as FDR) if "independent filtering" is enabled in Advanced Options:

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"Independent filtering" tries removing some features with low expression in order to increase the statistical power. For such removed features, the p-value is reported but FDR and similar multiplicity adjustment measures are set to "?". In order to avoid the missing values in the report, set the option to "No".

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

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