I have two Intereventions (HIgh protein and low protein diet) which i fed to individUals for 10 weeks, so i have 2 time points (PRE AND POST) . Simply i have 4 groups
Pre , Post Low diet, pre and post high diet.
i used deseq2 using this code
ddsTC <- DESeqDataSetFromMatrix(countDatanew, colData=phenotype_data, ~ intervention + Time + intervention:Time)
ddsTC$intervention <- relevel(ddsTC$intervention, ref="control")
ddsTC$Time <- relevel(ddsTC$Time, ref="pre")
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ intervention + Time)
and i was wondering does my formula takes into account within subject comparison