Hi all, I am using DESeq2 for a DE analysis from RNASeq data. I am not sure I am using the correct formula in DESeq2 for the analysis.\ I have 100 tumor samples and 100 normal-matched.\ The tumor samples can be subgrouped according their tumoral stage (I, II, III and IV). I am running DESeq assigning "N" as tumoral stage variable for all normal samples and then running the following design:

dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Patient_ID+Stage)

After that I extract results for the group comparisons

res <- results(dds, alpha=0.05, lfcThreshold = 0.58, contrast=c("Stage","I","II"))

I ignore comparisons against normals because I am interested in the differences between tumors from stages (but also keeping into account the inter-individual correction given by the presence of normal-matched samples).

Am I doing right?\ Thanks\ Matteo

It's one way of doing it, yes. The vignette is a good place to start, but for hands-on guidance on your exact analysis you might seek a local collaboration as this is not what the support site is for.