Hello!
I have 6 RRBS samples that I am analyzing in MethylKit. After looking at the clustering and PCA plots it seems that there are batch effects. The 6 samples were done at 3 different times, each time one control and one case. The samples cluster according to these batches.
How can I remove the batch effects with SVA or other tools? I looked at the assocComp function and there were 3 PCA components that seemed to be correlated with batches at the 0.1 - 0.2 level. I don't trust that removing those 3 components removes just the batch effects.
SVA is recommended in the documentation, but I'm not an expert in R and I'm not sure how to use with MethylKit.
I have 6 RRBS samples that I am analyzing in MethylKit. After looking at the clustering and PCA plots it seems that there are batch effects. The 6 samples were done at 3 different times, each time one control and one case. The samples cluster according to these batches.
How can I remove the batch effects with SVA or other tools? I looked at the assocComp function and there were 3 PCA components that seemed to be correlated with batches at the 0.1 - 0.2 level. I don't trust that removing those 3 components removes just the batch effects.
SVA is recommended in the documentation, but I'm not an expert in R and I'm not sure how to use with MethylKit.
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