Hi, I’m Alberto and this is my firs topic in this forum.

Recently, I’ve discovered mixOmics because I needed to calculate a PLS-DA. But I think I’m doing something wrong.

I used the following command:

df3 ← mixOmics::plsda(df2, df1$disease, ncomp = 2, scale = TRUE)

But, in the plot, first PC have 2.83% while second PC have 3.06%. It is a little weird for me, because with PCA or PCoA, the first component always has the highest value. For this reason, I decided to do a test, with the first 100 components. I show a screenshot with two dataframes (I only show you the 10 first rows). The first is a df with the components as they appear in the analysis. The second is after ordering the components by their percentage value.

Can someone explain to me why this happens? and how do I solve it?

Thanks!