I've a question concerning DESeq2. I've a multi-factor design as follow :
samples condition type Sample_A1 untreated X Sample_A2 untreated X Sample_A3 untreated Y Sample_A4 untreated Y Sample_B1 treated X Sample_B2 treated X Sample_B3 treated Y Sample_B4 treated Y
so I do
dds <- DESeqDataSetFromHTSeqCount(sampleTable=samples,directory="./",design= ~ type+condition) dds <- DESeq(dds) res <- results(dds)
In the results, I wonder how the log2foldchange is computed ? How it takes into account this two-factor design ?