Hello, We have mouse RNA-seq with 6 time points over 24 h period and 3 replicates for each time points (18 samples total), each sample is from different mouse, all measurements were performed as one experiment. PCA plot on all genes (below) shows that there are substantial variations between samples (often larger than between time points). This is probably biological variations, since circadian genes show robust rhythm, not much noise. I used BooteJTK to detect rhythmic genes and detected 117 significantly rhythmic genes. The low number of rhythmic genes is probably related with sparse data (only 1 day measurements with 4h intervals). I was asked to perform batch correction to group samples belonging to the same time point together. Would this be appropriate to use Combat? I saw some warnings that it should be used only when there are clear batches, but in our case each sample comes from different mouse, all time points are correlated for rhythmic genes, so I am not sure whether we have any batches and should use batcg correction at all. I would be grateful for any advice/comment on whether we can do batch correction and if so, what is the appropriate tool. Best regards Alex PCA plot image: https://photos.google.com/share/AF1QipOM-INBAqwGmTIRt6UWxrZOfPFQvljybcl8912caYyqgzjzQLUuBo4w8s36cUGHRQ?key=YTJ6ZTBBaHQyVUxxNWZKOVZJQ3A1WlZVbVBGV2ZR
First of all, did you normalized your data?