Hi, I read a lot of papers and I found that they didn't indicate what kind of values are used in t-test or logistic regression. Here is part of my data. The miR-29b-3p is the target gene and RNU48 is the internal control in my study. The dCT is calculated by CT of miR-29b-3p minus CT of RNU48.

ID  Response    CT of miR-29b-3p    CT of RNU48   dCT   2^-dCT
1   good        21.82               21.62         0.20   1.15 
2   poor        20.87               20.93        -0.07   0.95 
3   good        21.98               19.94         2.04   4.11

I want to find differentially expressed genes between patients with good treatment responses and patients with poor treatment responses. So, should I use dCT or 2^-dCT to perform the t-test and logistic regression to predict their response? I built a logistic regression model and I found that the AUC is smaller if I use 2^-dCT to compute. But, if I use dCT, the AUC increased from 0.65 to 0.75. I don't know which is correct. Correct me if I am wrong. Please help me, thank you.

This support site is intended to help people with questions about Bioconductor software, not general statistical questions. You should try asking your question at biostars.org, where it would be on topic.