Entering edit mode
Hello. I have a question regarding the results(dds) function for DESEQ2.
I have two conditions I am comparing: Knockout vs Young.
After performing summary of my Deseq analysis,
res <- results(dds)
res
summary(res)
I get young vs Knockout as default. Does this mean the young and KO groups were numerators and denominators in the analysis, respectively?
If I use the code:
resKO_vs_Young <- results(dds, contrast = c("Group", "Knockout", "young"))
Would this allow me to compare the knockout/young expression?
I am trying to interpret the resulting heatmaps and wanted to clarify the results of my code. Thank you so much for this wonderful tool.
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your contrast is not relevant. The only difference due to using Young - Knockout or Knockout - Young is the sign of the logFC. Nothing else changes, and certainly not the resulting heatmap since it is based on the underlying gene expression levels and doesn't incorporate any information from the linear model.