Hot answers tagged

1

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.


1

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.


1

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.


Only top voted, non community-wiki answers of a minimum length are eligible