I would like to compare several conditions to a reference condition using DESeq2. Currently I am using the contrast option in the "results"-function as follows:
However in a manual I found that they actually take a subset. http://www.ebi.ac.uk/training/sites/...d-s.anders.pdf I found
My question is: Are both approaches still valid? And, what is the benefit of one over the other?
Thanks,
Rob
Code:
dds$condition <- relevel(dds$condition, reference) #Do the calculation dds <- DESeq(dds, betaPrior=FALSE) res <- results(dds, contrast = c('condition',selected_condition,reference))
Code:
#First we subset the relevant columns from the full dataset: > dds <- ddsFull[ , colData(ddsFull)$treatment %in% c("Control","DPN") & + colData(ddsFull)$time == "48h" ]
Thanks,
Rob
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