Question: Phylpseq to deseq2
gravatar for nabiyogesh
5 months ago by
nabiyogesh0 wrote:

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.

deseq2 • 85 views
ADD COMMENTlink modified 5 months ago by Michael Love25k • written 5 months ago by nabiyogesh0
Answer: Phylpseq to deseq2
gravatar for Michael Love
5 months ago by
Michael Love25k
United States
Michael Love25k wrote:

Again, take a look at the vignette and beginners workflow, which explain the LFC in detail.

ADD COMMENTlink written 5 months ago by Michael Love25k
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