I have RNA_seq gene expression data measured using two different technology (Illumina GA and Illumina Hiseq) for specific cancer type. I checked for the cross platform bias (batch effect) using PCA plot. it seems that samples of the each technology clusters togethers. so I think I have batch effect in my data.
What is the simple way to remove batch effect ? what it will do for me ? the expression values will change after removing batch effect ?