PCA and elbow plot

[ptranvan]

Hi,

I am having some difficulty understanding your elbow plot and how to choose the right principal component (PC) for downstream analysis as described in the following page:

https://hbctraining.github.io/scRNA-seq/lessons/elbow_plot_metric.html

On this page, you mention using the percentage of variation, but all the calculations are made using the standard deviation (stdev).

To use the percentage of variation, the calculations would be:

var_explained <- stdv^2
sum_var_explained <- sum(var_explained)
percent_var_explained <- (var_explained / sum_var_explained) * 100

This would change the results of co1 and co2.

Can you explain ?

Thank you.