Hi all,

I wanted to know if it is possible to remove 3 batches using "limma". I have sequencing data with three possible batch effects: age, gender and working sets.

As far as I understand, using limma's "removeBatchEffect" enables to remove only two batches categories by defining "batch" and "batch2"

removeBatchEffect(x, batch=NULL, batch2=NULL, covariates=NULL,
              design=matrix(1,ncol(x),1), ...)

Is there a way to remove 3 or more batches?

Best

Yes, you can use the covariates argument to remove any number of batch factors, see

• https://support.bioconductor.org/p/83286/
• https://support.bioconductor.org/p/60879/