Error in smooth.construct.tp.smooth.spec when analyzing RNASEQ with covariate

[pamonlan]

I am trying to analyze an RNASEQ dataset using the NBAMSeq package in R, but I am encountering an error when trying to include a covariate with 5 different points. The error message I am receiving is: "Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) : A term has fewer unique covariate combinations than specified maximum degrees of freedom."

I am unsure of how to proceed and would appreciate any assistance in resolving this issue.

[hhp94]

Hi @pamonlan, this is because the default basis function for {mgcv} (smooth.construct.tp.smooth.spec) sets k at 9 or something and your covariate only has 5 unique values. You can fix this by running design = ~ s(x, k = 4).