Closed svteichman closed 9 months ago
Good catch!
If I recall correctly, statdivlab/rigr
has a way to test contrasts. If we can turn a limma dependency into a rigr dependency, that would give us more control over failures.
Also, #$*& CRAN for removing all of these foundational packages!
It turns out the function works for and the examples/tests for this function weren't working. They've been fixed in PR #165 so I'm closing this issue.
I believe there is a problem with the use of the function
limma::makeContrasts()
called by the helper functionwaldchisq_test()
when runningcontrastsTest()
. There are two issues that I see:limma
has been removed from cran, and there is no error or warning when the package is not installed and the function is called, instead the function silently returns NAlimma
is installed (it is available on Bioconductor), running `limma::makeContrasts()" results in an error about an argument not able to be found, although no error or warning is thrown and the function silently returns NAI have currently added a warning to the
contrastsTest()
function that behavior is not as expected but I think this should be looked at in more detail.