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Which axis to look for in PCA plot to understand the sample clustering

Hi all,

I have four replicates for early and late lactation stages each. I did rlog transformation of the htseq counts and did PCA as a QC step to know whether the biological conditions cluster together. I obtained the attached PCA plot. Now I have a confusion on the axis I have to look for. As in the image, on PC2 axis the early and late stages cluster among themselves, but on PC1 they don't not. Can anyone please advise me the axis I should consider first?. Thank you!

please find the image here

pca rna-seq qc clustering
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updated by swbarnes2 swbarnes2 • written by kousi31 • kousi31

Hi Koussi31, I couldn't never explain better as this guy on you tube

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written by Morris_Chair Morris_Chair

1 answer

The link to google photos doesn't work.

PC1 is mathematically more important than PC2. You should try and figure out what PC1 corresponds to. Age? Where the sample was taken? Who prepped the RNA? Contamination with other tissue? Whatever it is, it would seem to be more important to your samples than the early or late stage.

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written by swbarnes2 swbarnes2

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