Hi, I have a RNA-Seq experiment and I'm wondering at which point I should exclude samples from my analysis? I couldn't find a good answer with googles help.
I clearly see (at least I would say it) in the sample-to-sample distance heatmap and a simple PCA-plot that one of my samples within one of the treatment groups differs from the other samples of the same group. But is there a threshold which I can use to say "yes" or "no" to the exclusion?
Please find attached both plots. The guy in the bottom left corner of the PCA-plot is the sample "SD_2" (see Distance plot).
Thanks for your help in advance.