Bioinformatics systems benefit from the use of data mining strategies to locate interesting and pertinent relationships within massive information. For example, data mining methods can ascertain and summarize the set of genes responding to a certain level of stress in an organism. Even a cursory glance through the literature in journals, reveals the persistent role of data mining in experimental biology. Integrating data mining within the context of experimental investigations is central to bioinformatics software. In this paper we describe the framework of Probabilistic Principal Surfaces, a latent variable model which offers a large variety of appealing visualization capabilities and which can be successfully integrated in the context of microarray analysis. A preprocessing phase consisting of a nonlinear PCA neural network which seems to be very useful to deal with noisy and time dependent nature of microarray data has been added to this framework.