Affymetrix Junction Arrays

AltAnalyze is capable of immediately analyzing Affymetrix files from several Affymetrix junction array platforms. These microarrays probe both known and predicted exon-exon junctions as well as known and predicted exon regions. Expression analysis is conducted similar to exon array analyses by processing the Affymetrix CEL files using RMA (via an automatic call to APT) and examining probeset-level versus gene-level differences for the different array features. Currently, three array platforms are supported, the JAY array, hGlue array and AltMouse array. Details on the analysis methods used for these platforms are available in the associated platform links. For users analyzing a different junction array, see this page.