I have a seurat object with 10 samples (5 in duplicates). I have added them all together and created the
VlnPlot to check for the quality of the samples.
As one can see in the pic below, the quality is quite different in each of the duplicated conditions. I was wondering, if it make more sense to find subsetting parameters which will comply with all the samples, or one can do it one sample (or one condition) at a time by itself.
What is the best way to proceed?