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!