Recently I am trying to analyze some RNA sequencing data and perform the differential expression analysis. Since the sequencing data were generated in different times (experiments), I am worrying about the potential batch effects and would like to find a way to figure out and remove it (remove is more important!)
I tried to process the data in two different ways: 1) Obtain the RSEM values and perform the differential expression analysis, in this way, can anyone kindly provide a good tool to apply on RSEM values to remove the batch effect? 2) Obtain the htseq raw counts and use Deseq2 to perform the differential expression analysis. I saw previously another discussion about about justifying the batch effect by adding the 'batch' in the 'design' [design ~ batch+treatment] parameter in Deseq2. Besides this, can anyone kindly provide another good way to remove the batch effect?
Thanks for the help in advance.