When I try to run this portion of code i receive the error:

> colnames( counts ) <- paste(c(rep("Gene.ID",1),rep("Reads.Count",1)),sep=",") # sample names
Error in `colnames<-`(`*tmp*`, value = c("Gene.ID", "Reads.Count")) : 
  'names' attribute [2] must be the same length as the vector [0]

the files in question are csv's and they have 2 columns. 

Thank you for your help.

This question has nothing to do with edgeR, but is instead a general R question. And you don't give enough information for anybody to help you. But if I rummage around in R, I get this:

> counts <- data.frame()
> colnames(counts) <- paste(c(rep("Gene.ID",1),rep("Reads.Count",1)),sep=",")
Error in `colnames<-`(`*tmp*`, value = c("Gene.ID", "Reads.Count")) :
  'names' attribute [2] must be the same length as the vector [0]

Which makes me think that you have somehow instantiated an empty data.frame and are now trying to put column names on it. You need to actually have a two-column data.frame first! Note as well that

colnames(counts) <- paste(c(rep("Gene.ID",1),rep("Reads.Count",1)),sep=",")

is a more, um, verbose way of doing

colnames(counts) <- c("Gene.ID","Reads.Count")

If you have two-column files containing counts, perhaps you should be using the readDGE() function to read them into R and edgeR?