What files do I need when analyzing Affymetrix arrays?
Answer: If you are analyzing any human, mouse or rat Affymetrix arrays, only your CEL files are needed. However, for many other Affymetrix species arrays, AltAnalyze will automatically download the dependent library and annotation files. This process is not perfect, since some CEL files have addition encoding which can hinder proper identification of which array type the array is. However, users can always download any other library and annotation files needed to analyze and annotate your array results. Library files are needed to perform RMA summarization and annotation files are needed (with the exception of Exon 1.0, Gene 1.0, JAY and AltMouse arrays) to add probeset and gene annotations to your results.