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interprating PCA plot

Hello, everyone here,

I am doing diff. expression analysis using DESq2. I used PCA() function to show sample clustering as a QC. However, the figure I got seems difficult to interpret. I wonder someone could help me in the interpretation of the figure? The four colors in the picture represent four phenotypes(A, B, C, and D). The shapes(circle and diamond) are gender(m and f).

PCA plot

Thank you!

pca rna-seq
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updated by ATpoint ATpoint • written by adR adR

Life goals: have our names used as a keyword on Biostars :D

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written by Mensur Dlakic Mensur Dlakic

Yep, indeed, there's now nothing else in life for me to achieve ;)

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written by Kevin Blighe Kevin Blighe

2 answers

There seems to be a dramatic batch effect - PC1 is dominating the variance, but the effect is not clearly related to the phenotype. So, perhaps just difference between individual donors (very common in human studies, esp. for bulk tissue like whole blood or PBMC).

Also, PC2 is very much correlated with gender.

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written by predeus predeus

As so you have something to compare to, I was looking at a data set of mine which compares healthy samples to samples with a serious genetic disease...where you expect the first PC to be the difference between healthy and diseased, and you expect it to be a very large % of the variance, and in my case that was true, PC1 was 76% of the variance.

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written by swbarnes2 swbarnes2

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