I'm trying to run the following function

qval <- qvalue(DE.object$p.value[, 2], fdr.level = 0.05) 

And I get this error:
Error in density(x, adjust = adj) : unused argument (adjust = adj)

Can anyone help? Would be greatly appreciated

Thanks!

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

It's likely that stats::density.default got masked by a package that you loaded, and now the masking density function is being called, and it doesn't have an 'adjust' argument. You will get messages when functions are masked by package loading. As an example, here is what happens when I load dplyr

> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff,
    setequal, union

And now if I try to use base::union without using the qualified name, I will get dplyr::union instead. If qvalue called stats::density directly it wouldn't be a problem, but it's not super common IME for people to write code that includes the qualified name for every function used (I sure don't do that...).