**570**wrote:

Hello,

I have the following (certainly not ideal) RNA-seq experimental design:

- Batch 1 contains 40 samples with condition A + 12 samples with condition B
- Batch 2 contains 40 samples with condition C + the same 12 samples with condition B

So, the 12 samples with condition B are technical replicates that have been profiled across the two batches.

I'm actually not interested in condition B; I need to compare the 40 samples with condition A from batch 1 with the 40 samples with condition C from batch 2.

Are there Bioconductor packages (or other methods/approaches) that will allow me to **use the 12 technical replicates profiled across batches to correct for batch effects** before performing a differential expression analysis?

I already came across RUVSeq (see this question) and I'm looking for alternative approaches.

Thank you!

**37k**• written 3 months ago by enricoferrero •

**570**