I do have three treatment: T1, T2 and T3: I am interested in all three pairwise comparisons. For that Should I need to make one of them as a reference or by using contrast I can get all three comparisons?
If I extract logfold change in below comparison what does it means: Up and down in T3 or T1?
diagdds = phyloseq_to_deseq2(root_M, ~ Treatment) converting counts to integer mode > diagdds = DESeq(diagdds, test="Wald", fitType="parametric") estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 2848 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing > resultsNames(diagdds)  "Intercept" "Treatment_T2_vs_T1" "Treatment_T3_vs_T1" > res-M-ROOT-T1.T3= results(diagdds, contrast = c("Treatment", "T1", "T3"), alpha = 0.1)
I will be very thankful for your help.