Error in estimating dispersion when fitting contrasts with EDGER using design Matrix

[ShaliniPandurangan]

Error in estimating dispersion when fitting contrasts with EDGER using design Matrix

[ShaliniPandurangan]

The error is from the following line in the ngs-fit.R file

https://github.com/bigomics/playbase/blob/025bc205823b24df5df1b2e3e854fbf8af42481a/R/ngs-fit.r#L617C17-L617C29

estimateDisp from edgeR uses the locfit package.

This error is explained here.

https://rdrr.io/github/bmansfeld/QTLseqr/f/vignettes/QTLseqr.Rmd#:~:text=When%20running%20either,selected%20window%20size.

It happens when the window size is set too small. So the options for the fix are increasing the window size or using other trend methods to estimate dispersion trend.

In the solution, I am using other trend method 'Lowess' instead of manually setting the window size.

This is the output after modifying the trend method.