I am working on my master's thesis and I am facing huge problems I cannot fix due to time and money problems.
I sent six samples of RNA to a sequencing company, 3 treated and 3 controls. And only two from each have passed their quality test. I am only testing one drug by the way.
I did differential gene expression analysis and got the results. I am only focusing on significant pathways, I will not focus on genes. From what I read genes are out of the question at this point.
My advisor says everything is ok but I think my thesis is a joke. Will I fail to defend my thesis?
I also did three apoptosis assays: Nuclear morphology by Hoechst 33324 staining method, acridine orange–ethidium bromide dual staining method, and Annexin-V/ propidium iodide apoptosis assay in flow cytometry.
Thank you tons, I asked this question before but without these details that might give me a different answer.