Hello, if you are able to help I would be so thankful!

I am using missMethyl to annotate my most significant DMPs of treatment response in a biomarker study. I have no significant DMPs but am continuing with this annotation anyway- this is part of the error message I am facing. I would still like to be able to see an object/table for toppaths (below), even if my top dmp/paths aren't significant. Is there any way I can do this?

Paths object is open in the right window and the console is on the left.

toppaths <-topGO(paths, paths$N, ontology = c("BP", "CC", "MF"), sort = NULL, number = 10L, truncate.term = NULL)

Error in if (p.value < 1) number <- min(number, sum(P <= p.value)) : the condition has length > 1

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Hi Grace,

Are you running gometh() to perform gene set testing? It is not clear what you are trying to do from the above comment. If you are doing gene set testing can you try the topGSA() function rather than the topGO() function? topGO is specifically from the limma package after running goanna().

I suspect that all your p-values are 1 and that is why you are getting the error message above.

toppaths <- topGSA(output_from_gometh, number = Inf)

You can also just look at the data frame that is outputted by gometh. The topGSA function simply ranks it by p-value. If all your p-values are 1 then you don't need to do this step as there is nothing to rank on.

output_from_gometh[1:10,]

Cheers,

Belinda