Normalization and Batch Effect of bulk RNA-Seq

Question

[hkarakurt]

Hello everyone, I have a question. Let's say I have 2 different RNA-Seq (bulk RNA-Seq not single cell) data from different research groups but they are the exact same biological sample (cell culture).

Both of the groups uses different experimental protocols, number of PCR cycles etc. and Illumina sequencers so there is a batch effect. As I know there are some methods to correct batch effect, but is there a normalization (or modified normalization) method that removes batch effect. I did not see any example but is it possible to use something like relativity based normalization that uses the library size of each sample?

Pre-process of the both datasets (alignment etc.) is same in this case.

Thank you in advance

Answer 1

[swbarnes2]

There are programs like combat and combat-seq, or removeBatchEffect in Limma which will remove batch effect. These are likely fine for visualizations.

But for some applications, this is not what you do. For finding differential gene expression, it's preferred to leave the data alone, and make batch an element of your design.