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:

![enter image description here][1]

Similarly, I also plotted a PCA with only `Gencode lncRNAs` which looks like below:

![enter image description here][2]

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.

Thank you.

[1]: i.imgur.com/bqEyS5M.png
[2]: i.imgur.com/P84dQAe.png

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