Removing batch effects from RPKM data

Question

[AB]

Hi everyone,

I am doing RNA-Seq data analysis on 22 samples from 3 batches. I have the RPKM values of all the samples. I performed PCA and I found some batch effect. I would like to remove the batch effect so that I can go ahead with differential expression analysis.

I was reading some posts and I saw that the removeBatchEffect() function in the limma package of bioconductor has been used a lot with count matrix. Can I use this function with a matrix containing RPKM values? In that case, will the result also be a matrix containing RPKM values with just the batch effects removed ? Also, should I take log2 values of the RPKM ?

Thanks,
Apoorva

Answer 1

[andrew.j.skelton73]

The short answer is no. I suggest you look at the discussions in your own post on Bioconductor Support: https://support.bioconductor.org/p/73595/