length scale

[ruqianl]

Hi Luke,

I'm wondering which column in the result represents the fitted length scales for each gene, or how to find it using the reported results.

Thanks

[boyiguo1]

I had the same question, and here is the answer I received from @lmweber:

The phi in the output, i.e. rowData(spe) is related to the length scale parameter.

Specifically, phi is the inverse of the scale length parameter. You can calculate the length scale parameter by l_nnSVG = 1 / phi_nnSVG

I think it would be great to have this documented in the manual or have the length scale parameter in the output instead of phi

[lmweber]

Thank you @ruqianl @boyiguo1 ! Yes, phi is the inverse of the length scale parameter l, in the parameterization that we use.

Yes, good idea, I could mention this in the vignette. I'll leave this issue open as a reminder to add it in the vignette.

[lmweber]

Also explain the 3 main fitted parameters (sigma.sq, tau.sq, phi / l) in both the package help files and vignette