I'm currently doing a differential expression analysis on RNA-seq data. After counting the reads with salmon, and normalizing with deseq2, I've plotted the dispersion of my samples thanks to a PCA.
I have 3 replicates per conditions, and I was kind of waiting for them to cluster together, but I found out that there is not really a clustering of replicates, the samples being spread across the PCA.
I'm not really familiar with this kind of output, and I was wondering if not seing clustering of replicates could be normal (due to biological variation between replicates,even with the sam conditions), or if I should worried about something before going to DE analysis.
Thanks for your inputs,