I am using DESeq2 Likelihood Ratio Test for multi-group comparison (6 different genotypes).
<h5>dds <- DESeqDataSetFromMatrix(countData = data, colData = meta, design = ~ genotype)</h5>
Likelihood ratio test
dds_lrt <- DESeq(dds, test="LRT", reduced = ~ 1)
As far as I know LRT doesn't use log2foldchange to calculate the p.value. Thus, I am interested to know how DESeq2 calculates these fold changes ( 6 genotypes in my case), and is there any way to interpret them.
PS. I would appreciate any link to the tutorial/paper on how to perform multi-group RNA-seq analysis and interpret it.