I have RNAseq data produced from multiple separate experiments that I want to analyze together. I would like to use BatchQC to evaluate the need and effect of batch effect correction. My understanding is that BatchQC requires "quantile normalized expression values". I have not been able to figure out how to perform this type of normalization. Is there an R package I can use to generate quantile normalized expression values"?

Thanks!

I've no experience with BatchQC but

library(preprocessCore)       #  implements normalize.quantiles