I am working with RNA-seq data, and I need to correct for covariates. To do this, I want to use the Bioconductor package SVA. I want to produce a 'corrected dataset' and then use this for further analyses - to perform pairwise Pearson correlations and generate heat maps to visualise co-expression. However, as I understand it, the documentation explains how to feed the covariates into a model for differential expression analysis, not how to produce and export a corrected dataset based on the SVA calculations.
I'd appreciate any advice on doing this, or in fact being informed that I'm going about this in the wrong way.