I've been running DESeq2 recently using the lfcShrink function i.e. lfcShrink(dds, coef=14, type="apeglm", lfcThreshold=0.1375). However, an error was returned i.e. unused argument (lfcThreshold=0.1375).
This has not occurred when I previously the same code above (some months ago). I'm wondering what accounts for the current error observation?
That argument didn’t go away. What could have happened is that you or a system administrator installed an older version of R/Bioconductor in which the argument didn’t exist. Check your package versions and check the versions on the Bioc website corresponding to release.
Thanks Michael. Yes, the version issue should be the reason. Currently run on a HPC with R/3.4.1., and previously on a local PC with a higher version of R. Thanks.