I am analyzing some RNA sequencing data from a collaborator where the effect of some ligands on the transcriptome is being looked at. I am using DESeq2 for my analysis. I am looking to compare each of the ligand treatments vs the DMSO. I have attached the MDS plot with this post. There seems to be a lot of variation between the 3 replicates across all the treatments. Based on this plot, is it worth it to use this data to run a differential expression?
It is also at this link below. https://imgur.com/a/HGHepl7