statOmics/tradeSeq

choosing knot

Closed this issue · 2 comments

AndreaYCT commented

Hi,

I have an integrated Seurat dataset and analyzed evaluateK() as attached pdf. I would like to know how to determine k in my case.

Many thanks

k result.pdf

koenvandenberge commented

Hi @AndreaYCT

In cases like this, where it is not consistent across the different visualizations, I often fall back to the first and third plot in your figure. Base on this, I would probably go for 6 knots as the AIC decrease after that becomes much smaller.

AndreaYCT commented

Thank you so much! I’m ready to proceed!

Hi @AndreaYCT

In cases like this, where it is not consistent across the different visualizations, I often fall back to the first and third plot in your figure. Base on this, I would probably go for 6 knots as the AIC decrease after that becomes much smaller.