# Tag Info

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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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sample is a character vector, so levels(dds$sample) is returning null. Presumably you mean to use dds$sample[1] here instead, which will likely solve the problem.

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You can try a hierarchical clustering tool HGC (hierarchical graph clustering). You may get cell population at different hierarchy by choosing multiple cutting heights. See the paper for more details.

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