Question: Plotting a PCA Plot from SVASeq results
0
gravatar for jjrin
10 months ago by
jjrin10
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 10 months ago by jjrin10
1

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

ADD REPLYlink written 10 months ago by genomax59k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 550 users visited in the last hour