Question: Plotting a PCA Plot from SVASeq results
gravatar for jjrin
8 months ago by
jjrin10 wrote:

Hello, I used SVASeq to remove batch effects in my data set.

I have run SVASeq and gotten 8 surrogate variables and all of the covariates necessary for my conditions. How would I plot a more detailed PCA plot rather than the give plot svseq function that is used in the vignette? I am thinking of something more along the lines of RUVSeq's PCA plots. I also have the DESeq results of my data that was used to generate the SVASeq covariates.

Thank you!

ADD COMMENTlink written 8 months ago by jjrin10

@Kevin's tutorial on PCA/biplots (and links there in).
PCA plot from read count matrix from RNA-Seq

ADD REPLYlink written 8 months ago by genomax57k
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