One of the methods for data quality assessment suggested in DESeq2 is to apply sample clustering. I have an RNASeq experiment with 8 treated and 6 untreated samples. All samples have good data quality metrics according to FastQC. But when I plot the heatmap of "rlog" transformed data, below is what I get. Unlike what I would expect, samples are not clustered by treatment quite nicely. However, they don't look too bad either!
I wanted to ask your expert advise. What would you do in this case? Will you exclude some samples from DE analysis, or include all but try to apply a method to eliminate batch effects, such as "svaseq"?
Thanks for your help in advance!