Hi

I have a question regarding RNAseq data analyses by DESeq2,

I have some data with 3 conditions (A, A1, D) and 3 other factors (P, B, Sex) with 2 or 3 levels in each,

my question is that if I use LRT without any contrast, is that correct to imply whatever results give me as a final output for comparison across these 3 levels in my condition,

I used this code: 

ddsMF <- DESeq(dds, test="LRT", reduced = ~ P + B + Sex, parallel=TRUE)
summary(ddsMF)
res_A_D_July17_ncon <- results(ddsMF)

2- if not, how a two-way comparison of DESeq2 is able to tell me how different the 3 conditions are from each other,

I mean if I use A vs D, A1 vs D, A vs A1, what is the big picture to see all the differences across all the 3 levels of condition.

Thanks,

I can't tell what that LRT does because you didn't list the full design. The LRT tests whether the coefficients that are in the full design and not in the reduced design explain more of the variability in the counts than expected under the null hypothesis. If the coefficients in the full design that are missing from the reduced design are useful in explaining the variability in the counts then the gene gets a small p-value.

The LRT will tell you if there are differences across all levels of a factor, if you remove that variable from the full design to make the reduced design. Pairwise contrasts are just telling you about differences between the pair of levels.