Can I get gene-level expression results?
The current exon array analysis software allows for the aggregation of multiple exon level probe sets into a larger "meta probe set". PLIER signal estimates and DABG detection values are then computed for these meta probe sets. The definition and grouping of the exons into a gene can have a significant impact on the final signal value of a particular gene. Affymetrix recommends using the "core gene" grouping or the "full gene" grouping files to derive the gene-level signal that should most resemble the expression of the constitutive exons. See the "Gene Signal Estimates from Exon Arrays" white paper for more information.