I received RNAseq gene expression data that show batch effects for several technical confounders. I am performing a differential expression analysis using DESeq2, and have tried to add these effects as parameters to my design (~batch1+batch2+condition), but some of them are also linear combinations of the others, resulting in a model matrix that is not full rank.
Someone suggests the usage of tools such as Combat or SVA, but I am aware that transformed values are no longer integer count and I wonder whether the usage of these values will affects the DESeq2 outcomes.
What is the correct way to remove batch effects in this case?
Thank you very much!