'Combine' is the incorrect word here. RankProd compares lists of terms by the rank of their statistical significance. It does not combine expression values into a merged dataset, if that's what you want.
Take a look at Section 3.2 of the RankProd manual, where it states:
Data with multiple origins
In this section, we will illustrate how the RP method can be applied to datasets containing samples from multiple origins using the built-in data set arab. As mentioned before, arab consists of array data measured by two different laboratories. Both laboratories measured gene expression under the same two conditions.
Given the lack of experimental standards for microarray experiments, direct comparison is not feasible. Instead of using actual expression data, our approach combines the gene rank from different origins together (for details refer to Breitling et al. (2004)).
Thus, you can compare the results from your two Affymetrix microarray experiments. You may have to filter the datasets to only include common probe IDs prior to running RankProd, but you'll find out when you run it. It may also be advisable to summarise expression values over genes and/or transcript isoforms, and converting probe IDs to HGNC gene names, prior to running RankProd in this way.