All the code you have given (and even the comment) is identical to code in the vignette of Levi Waldron's LeviRmisc package:
except that you have incorrectly omitted the 'coef' argument from the topTable() call. I suggest that you study Levi's code and fix the call to topTable(). Try for example
Since you are working with Levi and obviously following his code, he would be your first point of call if you have problems. You might be confused by his pseudo code where he has given you a choice of options for the coef.
As for the error message, we cannot reproduce the error with any dataset that we have so we don't know what the problem is. I have asked you what version of limma you are using but you have not told me. As a first step, you could try updating limma and edgeR and see if it helps. If that doesn't work, then you could mail to me an RData file containing your
As Ryan has explained to you, you are actually using a mainly limma package DE pipeline. You have only used edgeR to create the DGEList object. All the other commands are limma. edgeR works with limma and limma is automatically loaded by edgeR.
Edit 3 hours later.
I can now see that you are using a recent version of limma on the devel repository, so the version isn't the problem. You should not be using topTable(fit) without specifying coef, because it is not appropriate for your data, but at the same time it should not give an error. If you want me to investigate further, please give a reproducible code example that I can run myself in which the required data is loaded as well as the code leading to the error.
If you are open to advice on your actual analysis, then the following code would be quicker and possibly better:
logCPM <- dpm(dge, prior.count=3)
fit <- lmFit(logCPM, design)
fit <- eBayes(fit, trend=TRUE, robust=TRUE)