The data are log2 transformed normalized intensities. Affymetrix arrays are single-color arrays that measure fluorescence intensity of the probes. So, there is not a concept of up- or down-regulation measured by a single array. To measure relative expression, one can look at the relationship between two arrays for a simple 2-sample experiment by subtracting the log2 intensities (the equivalent of taking a ratio). More commonly, one would use a statistical test to look for differences between two or more groups; often this is done using Bioconductor tools like limma.

Since you seem to be using R, I would encourage you to read the limma user guide. It is stocked full of useful general information as well as practical examples of working with affymetrix data.