Hi, I have a question related to the design of the experiment to perform differential gene expression. I have a RNAseq timeseries experiment of 468 samples at three different time points (T0, week12, week24) of only one cohort (diseased). I don't have two condition here but I have three timepoints of diseased condition. I am using DeSeq2 and I created design as follows. I am wondering if I am going in correct direction or not.
dds <- DESeq(dds,test="LRT", reduced = ~ 1) - Is this correct? dds <- DESeq(dds)
I am not getting errors either way. But I am not able to figure out which is more appropriate to my scenario. Any help is much appreciated.