Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays

Background: Normalization is an important step for microarray data analysis to minimize biological and technical variations. Choosing a suitable approach can be critical. The default method in GeneChip expression microarray uses a constant factor, the scaling factor (SF), for every gene on an array. The SF is obtained from a trimmed average signal of the array after excluding the 2% of the probe sets with the highest and the lowest values. Results: Among the 76 U34A GeneChip experiments, the total signals on each array showed 25.8% variations in terms of the coefficient of variation, although all microarrays were hybridized with the same amount of biotin-labeled cRNA. The 2% of the probe sets with the highest signals that were normally excluded from SF calculation accounted for 34% to 54% of the total signals (40.7%

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Chao Lu
• Keywords: BMCBI 2004, Expression Microarrays, GeneChip Expression Microarray, Total Signals