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Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability
September/October 2011 (vol. 8 no. 5)
pp. 1425-1430
Paolo Magni, Università degli Studi di Pavia, Pavia
Angela Simeone, (BIOTEC), Technische Universität Dresden
Sandra Healy, National University of Ireland, Galway
Antonella Isacchi, Nerviano Medical Sciences, Nerviano
Roberta Bosotti, Nerviano Medical Sciences, Nerviano
Microarray experiments are affected by several sources of variability. The paper demonstrates the major role of the day-to-day variability, it underlines the importance of a randomized block design when processing replicates over several days to avoid systematic biases and it proposes a simple algorithm that minimizes the day dependence.

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Index Terms:
Gene expression, statistical analysis, Affymetrix microarray, experimental variability.
Paolo Magni, Angela Simeone, Sandra Healy, Antonella Isacchi, Roberta Bosotti, "Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 5, pp. 1425-1430, Sept.-Oct. 2011, doi:10.1109/TCBB.2010.82
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