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Microarray data analysis involves several distinct steps, as outlined below. Changing any one of the steps has the potential to change the outcome of the analysis, so the MAQC Project<ref>{{cite web | url = http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/ | title = MicroArray Quality Control (MAQC) Project | accessdate = 2007-12-26 | author = Dr. Leming Shi, National Center for Toxicological Research | publisher = U.S. Food and Drug Administration }}</ref> was created to identify a set of standard strategies.
==Creating raw data==
Most microarray manufacturers, such as [[Affymetrix]], provide commercial data analysis software with microarray equipment such as plate readers. Raw Affy data contains information about mismatch spots, spots which do not precisely match the target sequence. These can theoretically measure the amount of nonspecific binding for a given target, but some popular approaches like RMA do not take advantage of them.<ref>{{cite journal |author=Bolstad BM, Irizarry RA, Astrand M, Speed TP |title=A comparison of normalization methods for high density oligonucleotide array data based on variance and bias |journal=Bioinformatics |volume=19 |issue=2 |pages=185–93 |year=2003 |pmid=12538238 |doi=}}</ref>. The current Affymetrix MAS5 algorithm, which uses both perfect match and mismatch probes, continues to enjoy popularity and do well in head to head tests.<ref>{{cite journal |author=Lim WK, Wang K, Lefebvre C, Califano A |title=Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks |journal=Bioinformatics |volume=23 |issue=13 |pages=i282–8 |year=2007 |pmid=17646307 |doi=10.1093/bioinformatics/btm201}}</ref>
==Background correction==
Depending on the type of array, signal related to nonspecific binding of the fluorophore can be subtracted to achieve better results. One approach involves subtracting the average
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