An exciting feature that distinguishes immunomic from DNA microarray data is the possibility of measuring two or more signals simultaneously, determined by a single feature, the epitope. In the case of DNA microarrays, one response value is obtained for each gene per sample, namely the concentration of mRNA produced by the gene (note that twodye experiments use mRNA from two different samples). In the case of peptide-MHC chips, a single epitope can generate different response values corresponding to different cytokines or different target T cell populations, or even different antibody isotypes, in the case of peptide microarrays. In other words, in the case of genomic microarrays, one parameter is measured, namely the level of transcription of each individual gene, whereas in the case of immunomic microarrays, it is possible to measure several parameters regarding immune responses against a single epitope. For instance, a single B cell epitope can be recognized by different isotypes of immunoglobulins, such as IgE or IgG1. Therefore, in this case it is not only the intensity of the antibody response that can be measured, but also the quality of the antibody response. This aspect can be very relevant since a high IgE titer in relation to IgG1 may be associated with allergy, whereas the opposite, a high IgG1 titer in relation to IgE to the same epitope, is not. This situation is even more significant in the case of the peptide-MHC array, where the same peptide-MHC epitope can induce several different cytokine responses. These ''multicolor'' peptide-MHC microarrays have a counterpart in the multicolor ELISPOT assays currently in use [101] . It is known that the combined effect of multiple cytokines is essential to the control of immune responses; this is described by the suggestive term ''cytokine chord'' in [102] . Thus, given a family of epitopes, one may want to simultaneously measure both inflammatory (effector) and anti-inflammatory (regulatory) T cell responses, which are known to be associated with the concentrations of IFN-c and IL-10, respectively [103] . In this case one would have more than one spot on the microarray containing the same epitope (peptide-MHC complex) but use distinct cytokine antibodies for detection (see Figure 3 ). The result of this analysis is not a real-valued profile, as is obtained from functional genomics microarrays, but rather a vector-valued profile. Such profiles are sometimes called ''multispectral'' profiles (see the section on data analysis below). We will, however, adopt the term ''multicolor'' when referring to immunomic data, due to the fact that this term is already used in the similar setting of ELISPOT assays.