SoupX tutorial: meta.data nCount_RNA contains information from previous RNA assay

[KriBaLin]

Hi, thank you a lot for your SoupX tutorial. I find the video and the code very helpful during my own analysis since I am new to scRNAseq analysis. One thing that I stumbled upon is that the nCount_RNA is not "updated" when I adjust the RNA assay of the seurat object with the SoupX-filtered counts. I'm referring to line 94 (sobj@assays$RNA@counts <- out) of your .Rmd file in this repository. I noticed this when I tried to check whether counts actually changed by summary([email protected]$nCount_RNA == [email protected]$nCount_original.counts) and nothing had changed. When I tried to overwrite the RNA assay with sobj[["RNA"]] <- CreateAssayObject(counts = out) nothing changed. When I do this giving a new name to the assay, e.g. with sobj[["RNAsoupx"]] <- CreateAssayObject(counts = out) it works.

I'm not sure if this is the right place to post my observation/question, maybe you have an idea how the [email protected]$nCount_RNA information can be updated by maintaining the name "RNA" for this assay. I'm not sure whether giving the assay a new name could cause any problems during downstream analysis.

Thank you a lot :)