I'm attempting to compare total RNA-seq with Ribo-Seq, to determine if changes in Ribo-Seq are due to changes in transcriptional expression (akin to the analysis performed by Anota2Seq). I am, however, struggling to understand how to accomplish this in DESeq2.
My design is as follows:
cts <- read.delim("Interaction.txt", row.names=1) coldata <- read.delim("Sample_Sheet.txt", row.names=1) cts <- round(cts) dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~Genotype + Type + Genotype:Type) dds <- DESeq(dds) resultsNames(dds) > coldata Genotype Type C_24h_Ribo_1 Control Ribo C_24h_Ribo_2 Control Ribo C_24h_Ribo_3 Control Ribo CHIK_24h_Ribo_1 Viral Ribo CHIK_24h_Ribo_2 Viral Ribo CHIK_24h_Ribo_3 Viral Ribo C_24h_RNA_1 Control RNA C_24h_RNA_2 Control RNA C_24h_RNA_3 Control RNA CHIK_24h_RNA_1 Viral RNA CHIK_24h_RNA_2 Viral RNA CHIK_24h_RNA_3 Viral RNA > resultsNames(dds)  "Intercept" "Genotype_Viral_vs_Control" "Type_RNA_vs_Ribo" "GenotypeViral.TypeRNA"
I do not understand which contrast is the one I need, or how to access the results i'm looking for (or interpret them). Any help?