I am trying to generate an MA plot with the following code:
dds <- DESeq(dds) res = results(dds, contrast=c("group","Control","653")) resultsNames(dds)# this returns 'Intercept' 'group_653_vs_111' 'group_Control_vs_111' plotMA(res, ylim = c(-5, 5))
This returns a plot with one vertical line that stretches from the max of the y-limit to -2 @ x=0.
Has anyone seen this before? If so, do you have any insight to resolve the issue? I imagine it is a problem with my data, not with DESeq2 per se.
Thank you in advance for your help!