RUVseq in

I have 12 samples in total - 2 genotypes, and 4 treatments, 3 replicates each. After running DESeq2, I see with the PCA plots that there is a strong batch effect - the samples from one genotype aggregate according to the batch of cells and not the treatments.
I am trying to use RUVSeq in but I am not sure how. As factors, should I input genotype, treatment and the batches as well?

Thank you!!!


Hi @CarolMCam,

these kind of known or easily inferred batch effects can be accommodated by DESeq2 without using RUVseq.
You can add multiple factors (not factor levels) in the DESeq2 wrapper by clicking on Insert Factor. The first factor is the primary factor, so should probably be treatment. You can then add a genotypes and batch information as secondary and tertiary factors.

If you want to use RUVseq in Galaxy you would only use the primary factor levels and let the algorithm find the batch factors that you can then use in DESeq2.

Hope that helps,

Thank you so much, Marius! I will try both and see what happens!

Have a great week and thank you again.