Question: Which axis to look for in PCA plot to understand the sample clustering
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gravatar for kousi31
11 months ago by
kousi3110
kousi3110 wrote:

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

clustering rna-seq qc pca • 361 views
ADD COMMENTlink modified 11 months ago by swbarnes28.2k • written 11 months ago by kousi3110

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

ADD REPLYlink modified 11 months ago • written 11 months ago by Morris_Chair190
0
gravatar for swbarnes2
11 months ago by
swbarnes28.2k
United States
swbarnes28.2k wrote:

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.

ADD COMMENTlink modified 11 months ago • written 11 months ago by swbarnes28.2k
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