Normally I do it from non-pruned data. But if you do some light pruning, it certainly does not harm. Here I wanted to keep the workflow as straightforward as possible. To be honest, I did not try, but I would assume the plot is very similar when pruned and non pruned data is used.
@@GenomicsBootCamp Yeah, I think it's more of one of those "best practices" things that doesn't really matter much in terms of outcome. Not pruning may lead to some inflated (or deflated?) eigenvalues but shouldnt matter much in terms of looking for things like outliers and grouping by breed .
Thank you alot !!! . What you always brought via UA-cam is very basics and interesting area
Thank you so much for this benefit video, please make Marge different database genotype
Shouldn't we prune for LD prior to running the PCA?
Normally I do it from non-pruned data. But if you do some light pruning, it certainly does not harm. Here I wanted to keep the workflow as straightforward as possible.
To be honest, I did not try, but I would assume the plot is very similar when pruned and non pruned data is used.
@@GenomicsBootCamp Yeah, I think it's more of one of those "best practices" things that doesn't really matter much in terms of outcome. Not pruning may lead to some inflated (or deflated?) eigenvalues but shouldnt matter much in terms of looking for things like outliers and grouping by breed .