From fdf8a1346eadff5d870210bde0b64a425689e567 Mon Sep 17 00:00:00 2001 From: Tyler McInnes Date: Fri, 10 May 2024 09:46:07 +1200 Subject: [PATCH] collapsing formatting --- docs/episodes/5.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/episodes/5.md b/docs/episodes/5.md index 4411e9d..85a6a50 100644 --- a/docs/episodes/5.md +++ b/docs/episodes/5.md @@ -302,7 +302,7 @@ To choose the elbow point in our scree plot, we can use the following: ##### Permutation - We do not demonstrate this method, as it is more code intensive. The idea is to permute (or “shuffle”) a subset of the data, rerun the PCA and calculate the percentage of variance explained by each PC on this “random” dataset. We can then compare the observed variance explained in the original data with this null or random expectation and determine a cutoff where the observed variance explained drops to similar values as the variance explained in the shuffled data. + We do not demonstrate this method, as it is more code intensive. The idea is to permute (or “shuffle”) a subset of the data, rerun the PCA and calculate the percentage of variance explained by each PC on this “random” dataset. We can then compare the observed variance explained in the original data with this null or random expectation and determine a cutoff where the observed variance explained drops to similar values as the variance explained in the shuffled data.
![image](../r_images/featureselect-permutation.png){width="500"}
In this example (which is for illustration only) we may define a threshold at PC8, since after that the variance explained in the observed data drops below the levels in the permuted (randomised) data.