Hi,
I want to apply edgeR to an RNA-Seq transcriptomic dataset. But I also want to apply the combat algorithm to different batch samples that include time points and differences in extraction. I have reviewed publications on technical and biological replications, but I am having trouble designing and my PCA analyzes are not successful. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are independent samples. There is no time course. Sample Id's represent the same patient. First comparison should be between control and infected by edgeR. Then I need to make comparison between high viral and low viral load with edgeR. But since the difference days and different library extraction I need to apply combat algorithm for batch correction.How should I design the batch column to apply the combat algorithm base time point?
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write down which questions you want to answer. Then we see how to encode that. What is "day"? Is this a timecourse?