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

Question

[kousi31]

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

[Morris_Chair]

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

Answer 1

[swbarnes2]

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.