waldchisq_test - silently fails when limma is missing

statdivlab / corncob

Count Regression for Correlated Observations with the Beta-binomial

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waldchisq_test - silently fails when limma is missing #98

Closed AdrianS85 closed 3 years ago

AdrianS85 commented 4 years ago

Dear Bryan,

I noticed that contrastTest was not giving me any results. After looking into the problem I noticed that waldchisq_test is interrupted at this line when limma is missing:

https://github.com/bryandmartin/corncob/blob/338323e9dfd303abe16ddcc582199f8028ccb14c/R/wald.R#L118

No indication that something went wrong is given. Hope it's relevant and helps!

Best Adrian

bryandmartin commented 4 years ago

Thank you! This is very helpful. Can you please elaborate on what you mean by not giving any results?

AdrianS85 commented 4 years ago

Of course, sorry : ] All p/p_fdr values returned by the functions were NA. This was not the case after installing limma.