1. A method for analyzing data generated by probe arrays, comprising: (a) receiving a first user selection of at least two data files and a second user selection identifying one or more subsets of intensity values within each data file, wherein each subset comprises one or more of the intensity values acquired from a biological probe array; (b) opening one of the data files; (c) identifying the intensity values associated with one or more of the selected subsets; (d) determining one or more parameters for processing; (e) storing the parameters and the identified intensity values; (f) closing the data file; (g) repeating steps (b)-(f) for each of the selected data files; and (h) processing each of the stored intensity values using the one or more parameters to identify one or more biological events.