What are the basic quality assessment metrics for the Exon Array?
The standard Affymetrix expression control sets (i.e., bacterial spikes) including both the hybridization control spikes and poly-A RNA control spikes are present on the Human Exon 1.0 ST Array and can be used to assess quality in a qualitative manner as used previously. As a new feature unique for the Exon Array, the Expression Console software supports the extraction of residuals from the PLIER model when running a multiple-array analysis. Such residuals can be used to identify outlier arrays and poor performing probes. In addition, for most of the 100 normalization control genes used in the design of the GeneChip® Human Genome U133 Array, probe sets representing both their intron and exon regions have been tiled on the Exon Array. The exon and intron probe set metrics (i.e., % detection p-value Quality Assessment of Exon Arrays” white paper for more information.
