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.