<p>Does anyone know of a reliable package for doing pairwise DE analysis on microarray data in the form of an ExpressionSet object? I&#39;ve used edgeR before for doing pairwise comparison with rna-seq, but I&#39;m a little new to this and can&#39;t really find anything to do it on affy data specifically...</p>

I use *samr*:

R. Tibshirani, G. Chu, Balasubramanian Narasimhan and Jun Li (2011). samr: SAM: Significance Analysis of Microarrays. R package version 2.0. http://CRAN.R-project.org/package=samr

Expression data are a matrix E, with identifiers PROBE_IDENTIFIERS and symbols GENE_SYMBOLS, and labels indicating pairs. Labels are integers starting at 1, with positive or negative indicating paired samples. Works for any array (or indeed any matrix of numbers).

```
data = list(x=data.matrix(E),
            y=labels,
            geneid=PROBE_IDENTIFIERS
            genenames = GENE_SYMBOLS,
            logged2=TRUE)
samr.obj = samr(data, resp.type="Two class paired", nperms=100)
```