IronChip analysis work flow. (A) Flow chart of ICEP data processing and evaluation. Data evaluation with ICEP is organized into three functional modules: Single feature, EST and transcript evaluation. (B) In our application example, hybridized microarrays were scanned on a GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA) and processed (feature background subtraction and normalization) by the ChipSkipper software . ICEP uses these output files (generic tab-delimited text tables containing the normalized signal intensity and background data) for further analysis.