I am working with a cancer type dataset. There are in total 250 samples. All these samples are classified into 6 groups. And I plotted a PCA plot with
Gencode Protein coding genes and it looks like below:
Similarly, I also plotted a PCA with only
Gencode lncRNAs which looks like below:
Why the second PCA which is with only Gencode lncRNAs look completely different from first PCA? What is the reason? Can anyone please explain clearly about this.