A while ago I asked how to treat 3 samples per individual (ID) in a DESEQ2. It was recommended to use Duplicate Correlation in limma. I wonder how to combine both packages:
I run my DESEQ2 with
dds0 <- DESeqDataSetFromMatrix(countData = cts, colData = colData, design = ~ AGE+ DIAGNOSIS + SEX)
I see that the duplicate correlation is run with
dupcor <- duplicateCorrelation(vobj, design, block=colData$ID)
I struggle to combine both approaches here. Can give me a hint?
Unfortunately, I cannot find any example code online of someone using both approaches together.
Thanks so much, Bine