I am working on a project, and have been given a list of instructions as to how to analyze microarray data. I am to use the affy and affyPLM packages from Bioconductor.

I used ReadAffy() to read in my CEL files, then called rma() to normalize the data. I now that this function returns an ExpressionSet.

I was then told to use the affyPLM package to compute the RLE and NUSE scores in order to compute the median RLE and NUSE scores for each sample. However, I am unable to call any of the package's function (fitPLM(), NUSE(), RLE()) on the normalized data because it is an ExpressionSet. 

My question is, how could I utilize the affyPLM package to compute RLE/NUSE scores on an ExpressionSet, when the functions require the use of an AffyBatch.

To answer your question, directly, you cannot use NUSE and RLE on an ExpressionSet.

I'd suggest reading the vignette from affyPLM on Quality Control for details. That said, the ReadAffy() function returns an AffyBatch that you can then use for the affyPLM NUSE and RLE functions.