All experiments will be subjected to rigorous quality control assessments, generating a summary and detailed report of all QC indices that indicate the quality of the arrays. Initial low-level processing will consist of background assessment and normalization by RMA (robust multi-chip analysis), GC-RMA, or PLIER (Probe logarithmic intensity error) for the purpose of detecting and removing systemic variation and identifying potential problems with an array. This is necessary to enable better direct comparisons of microarray data. We employ primarily Affymetrix Expression Console™ for low level processing.
The high-level analysis seeks to identify differentially expressed genes and exons and expression patterns of distinct functional groups. In addition, we conduct thorough alternative splicing analysis for exon based experiments. The GCF has at its disposal several high end industry standards for high level analysis; Genespring, Partek, as well as academic license for Edge q-value optimized gene discovery software (University of Washington). Annotations will be done using standard platforms; Netaffix.
All reported analyses will be MIAME Compliance to better facilitate researchers in their publication goals.