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The object svobj$sv contains your new "Sequnator" variables. Add these to your DESeq2 design formula. Do not manually adjust the counts. Instead, include the surrogate variables in your statistical model:

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# Install BiocManager (if you don't have it) if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("sva") Load the library library(sva) The object svobj$sv contains your new "Sequnator" variables

Enter (often misspelled as "Sequator" in searches). This powerful tool, specifically the SVA package component (Surrogate Variable Analysis), helps you estimate and correct hidden batch effects when you don’t know what the confounding variables are. sequator download