Hi I'm trying to run differential expression using DESeq2 and I'm a little confused about how to interpret results based on contrast
. In my dataset I'm looking at 2 levels within my variable "stage" (B and R) and I want to visualize the results on a volcano plot.
I have created my DESeq object using the following code:
ddsWald_stage <- DESeqDataFromMatrix(countData = countData, colData = colData, design ~= stage)
I then created my results object using:
res_stage <- results(ddsWald_stage, contrast = c("stage", "B", "R"), cooksCutoff=TRUE)
When I plot this on a volcano plot, will genes that have significantly higher fold changes in the B group be on the right or left side of the plot? I'm a little confused by the documentation for contrast
. Any help would be appreciated!
Oh gotcha that makes sense. That was really helpful, thank you!
You are welcome, gpreising. Please do not work too much on Sunday (then you'll turn into me...).