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.