I am a newbie to transcriptomic analysis, so it would be grateful if anyone can help me out these issues.
I got a table of transcript abundance from a company has done transcriptomic analysis. First, I try with Deseq but an error came up, and it said my data is not integer so I can't proceed further. Then I tried to round up my data and it worked, but it seems like I lost quite a lot transcript information.
Second, I have 4 treatments, and 3 biological replicates per each treatment, in total, I have 12 samples. As following Deseq protocol, it uses nbinomTest (compare only 2 treatments), which test should I use for 4 treatments? I also tried with 2 treatments of my data, and the heat map still showed 4 treatments (12 columns) but not in order.
Third, how do I call the candidate genes from my data?
Does anyone have any idea about these issues?
Thank you and have a good day.