Doubt on whether blocking a variable in the linear model option for metadata comparisons

Hi all,

I am comparing two groups (A and S) which have repeated samples, pre- and post- treatment. There is also an age unbalance between. I would like to compare differences in metabolite abundance between A and S, irrespective of the pre- and post-treatment timepoint. I have already blocked the variable participant, so each participant is treated as a block. However, I’m unclear if I should still include age as a covariate in the model, my guess is that I should, but doing so markedly reduces the number of differentially abundant metabolites that I obtain.

I would highly appreciate any recommendations.

Thanks in advance!