Using SVA with RRBS data
Hello
I have seen a lot of posts with this question, but have not found an answer to this. I am analyzing my RRBS data with methylKit, and I can see in my PCA plots that there are some batch effects.
Is there a way to use SVA to estimate surrogate variables from methylation data? If yes, how to do that properly?
I have used it before with RNA-seq data, but am not sure on how to use with methylation data.
Thank you!
• 2,126 views
•
link
updated
by
Ram
•
written
by
mrodrigues.fernanda •
•
written
by
mrodrigues.fernanda •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Batch Effect Correction in RNA-seq Data Using SVA and DESeq2
written by Nelo •
-
Surrogate variable analysis: do I need to adjust all SVs?
written by wwyue127 •
-
How to remove batch effects using surrogate variables?
written by hansong798 •
-
Can't make sva comparison despite very distinct batch effects
written by jjrin •
-
Plotting a PCA Plot from SVASeq results
written by jjrin •
-
n.sv number for batch effects in RNA-seq
written by sophialovechan •
-
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
written by lessismore
-
Checking potential batch effects with svaseq
written by Tobias.Wohland
-
Find surrogate variables with svaseq()
written by Tobias.Wohland
-
sva + egdeR - differential expression analysis - RNA-seq data
written by mrodrigues.fernanda •
