In FNN::get.knnx(landmarklcms, idents, k = nlandmarks) k should be less than sample size

[EidrianGM]

When running msPIP function there is a point where the error mentioned in the title occurs.

I was wondering if the following is a valid solution:

nlandmarks <- min(50,nrow(landmarklcms))
# 50 because is the default of nlandmarks in the msPIP function 

The idea is to select the whole set of landmarks available in case that they are less than 50 to find the maximum number of nearest neighbors.

[soroorh]

thanks Adrian. I think you previously had other suggestions for msPIP. do you want to make a PR and i will have a look at your suggestions?

i think something like

nlandmarks <- min(nlandmarks, nrow(landmarklcms)) 

might be more robust/generic. but also have to have a closer look at the code!

Feel free to open a PR! thx

[EidrianGM]

Yes that is indeed better implementation but opens a new question for me regarding the methodology, which might not make sense but since you know better how to treat the proteomics data I wonder

Would be there any issue/implications when using different number of nlandmarks for each run/sample ??

[soroorh]

thanks for the question. msPIP in msImpute is very experimental and implementations were not fully evaluated. We are though experimenting with "number of landmarks" in a different but related project, and there we see it makes difference. But yes, generally given that the landmarks serve the purpose of between-run alignment, they should be shared across runs, where possible. but this i haven't tested in context of msImpute.

As i mentioned, feel free to suggest your changes in a PR. Happy to consider!

Hope this helps