Entering edit mode
23 hours ago
Megan
▴
50
Hi everyone,
I wanted to get some feedback on some DESEQ analysis I am currently doing. I have tried to run my pipeline and my PCA plot looks like this.
I have tried running it and I am getting little to no DEGS. Any advice would be greatly appericated.
So there's no difference. Reasonable result. Triple check your protocol and sample handling, did they get mixed up? Did they get processed correctly? Do you have gene expression of a reasonable level on genes you do expect to have active? This would be evidence of good RNA extraction.
The RIN values for these samples ranged around 6.0-7.0, which I think would suggest RNA degradation. From what I am aware of, I don't think that the samples were mixed up but I will double check that.
I doubt your RNA quality is the issue. It's not likely that poor quality would cause reads to align to the wrong gene. Its far more likely that your treatment has a very small effect.