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david.wheeler7
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@davidwheeler7-19959
Last seen 5.7 years ago
Hello!
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!
David
Thanks Michael,
Sure. here is the output from
res
after changing the order toresults(dds, contrast=c("group","653","Control"))
Do you see anything fishy?
This gave me a very similar MA plot
Can you use:
It may be that another package is masking our function.
Yes!!!! That did it!!! I do not understand the source of the error. If you have time, could please direct me toward the resources need to explain this? Thanks again Michael!
Some package masked plotMA. R will tell you in the console when this happens, you just have to pay attention to the loading messages.
Thanks Michael! I was running it in Jupyter Notebook and did not see anything. I will try again from the console.