Interpreting ellipses in PCAtools for bulk RNAseq

Question

[Elizabeth]

I had a quick question about using ellipses in PCAtools on bulk RNA-seq data. On my data, I can make a plot using the code below:

biplot(p, 
       lab = NULL, 
       legendPosition = 'right',
       colby = 'genotype', 
       colLegendTitle = 'Genotype',
# ellipse config
      ellipse = TRUE,
      ellipseLevel = 0.95,
      ellipseFill = TRUE,
      ellipseAlpha = 1/4,
      ellipseLineSize = 0)

As you can see, the WT group is circled and the CRE group has 2 lines drawn around it, rather than another circle, which I'm not sure how to interpret. Does this mean, that at the 95% confidence level, the CRE group isn't really one group?

For example, when I change ellipseLevel = 0.75, here's the output:

Since now all the points in the CRE group fall under the same circle, can I interpret that as I can be 75% confident all the CRE samples are statistically similar, or something like that? Just want to make sure I'm interpreting this correctly. Thank you!

[Ram]

Please ask this on bioC support - the developer has pointed to that forum as the place to ask questions: PCAtools: everything Principal Components Analysis

[Elizabeth]

Will do, thanks!

Answer 1

[Kevin Blighe]

Answered at: https://support.bioconductor.org/p/9137295/#9137297