I'm working on RNA-Seq datasets containing 22 samples from 3 batches. I used mm10 as the reference genome and generated the count table from the BAM files using GenomicAlignments package and then used the rpkm() function to get the rpkm data. Now I want to perform batch correction using either the count matrix or the rpkm data. How do I use the sva package for this purpose ? Is there any other way I can perform batch estimation and correction with the data I have ? Can i use removeBatchEffects() function or is it only for microarray data ?