DESeq2 lfcShrink option

[HelenaLC]

No description provided.

[mschilli87]

Thank you for continuing to maintain and further improve muscat. ❤️

[mertcan-demir]

Hi, thanks for adding this feature and still maintain the package! One thing I noticed, when lfcShrink = TRUE with apeglm, lfcShrink() returns s-values (if I am correct) in the padj slot, not BH-adjusted p-values. These then get renamed to p_adj.loc in muscat's output, which could mislead into interpreting them as standard FDR. Might be worth either documenting this or extracting the original p-values from results() separately when shrinkage is enabled.

[plger]

Hi,
Are you sure about this? lfcShrink() has the svalue argument set to FALSE by default (and we're not changing it), so it shouldn't actually do that, and in my hands the p-values and adjusted p-values are no different with/without shrinkage.

[mertcan-demir]

See now, you are completely right. I misremembered the default behavior of lfcShrink(), my apologies. Thanks for clarifying.