Is there too little variation to detect meaningful gene changes?

Question

[Megan]

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.

[karl.stamm]

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.

[Megan]

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.

[swbarnes2]

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.