Entering edit mode
Hi Michael,
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)
[1] "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.