You can perform batch effect removal with the sva R package. You can download the package and read its tutorial from its bioconcuctor page. In short, the package enables you to perform both "supervised" and "unsupervised" batch effect removal to transform your data, depending on whether the batch effected groups are known to you or not. Respectively, you can use ComBat() function and sva() function from the package to do the necessary transformation.

Typically you would first run something like PCA to see whether there is any evidence for a batch effect. If so then you can include the batch into the experimental design of for example edgeR, see Basic normalization, batch correction and visualization of RNA-seq data