Question

Detecting Outliers by looking at PCA

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3.7 years ago

leekun4 ▴ 10

Hi,

I performed the PCA analysis to see if there's any outliers in my analysis.

Here's the PCA plot

Is it safe to assume that samples that are plotted far-right side are outliers and exclude them from doing analysis?

Thank you for your help.

RNA-Seq R PCA Outlier • 1.8k views

ADD COMMENT • link updated 3.7 years ago by swbarnes2 14k • written 3.7 years ago by leekun4 ▴ 10

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Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

ADD REPLY • link 3.7 years ago by Ram 43k

score 0 · Answer 1 · 2020-08-31

You only have three male control samples; I wouldn't be that quick to throw one of them away. Maybe your controls really do have that much variation.

Can you see an obvious QC reason why those samples are like they are? Markedly lower % of mapped reads, markedly lower RIN score, anything like that? I'd ask the people who did the library prep if they noticed anything about those samples.