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The DESeq2 function collapseReplicates sums the counts for the technical replicates. Here is the code reference: github.com/mikelove/DESeq2/blob/master/R/helper.R#L186 OPs actual confusion was with the DESeq2 function plotCounts which by default normalizes count data and adds a pseudocount of 0.5 for plotting on log2 scale.


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