I am new in bioinformatics and have a background in neuroimaging where we often use a baseline to build our models. Meaning, all the relationships between variables (correlation or other measurements) are inferred from the difference of activity between or condition of interest and in the baseline. Although these types of differential models are gold standard in my field, I've heard that studies of differential co-expression in RNA-seq is controversed. Does anyone can explain me why (difficulty of choice of a baseline...etc) and/or point me to publications that discuss the topic?
Thank you very much!