Detecting Outliers by looking at PCA
Hi,
I performed the PCA analysis to see if there's any outliers in my analysis.
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.
1 answer
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.
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