Hi all, I have a RNAseq experiment to measure gene expression with 3 treatment and 3 control, but one of my treatment failed, now I just have 2 treatment vs 3 control. My question is that can I take another treatment sequenced in single end read to replace for one of my failed treatment? I am just beginner and have no experience in this area. I am much appreciated for your help.
The problem with adding samples post-hoc is that you're likely going to have a batch effect, due to different preparation dates. Sometimes you get lucky and this isn't a problem, but more often than not you're have a large number of genes different simply due to processing date in the lab. If your biological effect size is very large it may swamp out this effect. On the flip side, if your effect size is moderate or small then I would be very concerned that adding samples would simply increase noise and prevent you from finding anything significant.
Fewer more comparable samples is preferable to more less comparable samples.