Dear Michael,

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

If you don’t provide subject in the design then it doesn’t account for it. Can you paste your sample info table (colData) so we can see how the samples are distributed?