I have two RNAseq experiments that were run on the same type of samples, treated in two different ways and sampled over time.
So, experiment 1 has experimental groups:
Control (untreated) - Treatment A - 1 week recovery from treatment A - 4 weeks recovery from treatment A
Experiment 2 is
Control (untreated) - Treatment B - 1 week recovery from treatment B - 4 weeks recovery from treatment B
RNAseq was performed at different times, but using exactly the same protocol.
I have used DESeq2 to analyse the two experiments separately, but I now would like to merge and compare the two, but I am not sure what the best solution is.
I have tried to feed all of the aligned bam files to DESeq2, but if I then run PCA on the samples, they cluster by experiment and, most annoyingly, the controls do not overlap.
Any suggestions for how to proceed would be greatly appreciated. I am thinking maybe of something on the lines of what the Seurat package uses for integration of multiple scRNAseq datasets, but I am not sure whether that could be applied to my situation.