I'm looking to use the
plotHeatmap function from
scater package using a list of differentially expressed genes that have particular column labels for each cell (cluster labels). When I run differential expression using Seurat's standard method (Wilcoxon Rank Sum Test) then run
DoHeatmap(), it requires the SeuratObject to undergo
ScaleData before being able to call it for creating the heatmap. When I take the same list of differentially expressed genes and plug it into
plotHeatmap function in scater with the logcounts values from SingleCellExperiment object, I do not get the same "pattern" as what's generated by Seurat's
DoHeatmap function even though input genes and dataset is the same. I suspect it has to do with how I'm scaling (or not scaling) the data. My question is how exactly does Seurat scale data and can I replicate this with scater?