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Questioning the Utility of Pooling Samples in Microarray Experiments with Cell Lines

2006; SAGE Publishing; Volume: 21; Issue: 2 Linguagem: Inglês

10.1177/172460080602100201

1724-6008

Lara Lusa, Vera Cappelletti, Manuela Gariboldi, Cristina Ferrario, Loris De Cecco, James F. Reid, S. Toffanin, Giuseppe Gallus, Lisa M. McShane, Maria Grazia Daidone, Marco A. Pierotti,

Bioinformatics and Genomic Networks

We describe a microarray experiment using the MCF-7 breast cancer cell line in two different experimental conditions for which the same number of independent pools as the number of individual samples was hybridized on Affymetrix GeneChips. Unexpectedly, when using individual samples, the number of probe sets found to be differentially expressed between treated and untreated cells was about three times greater than that found using pools. These findings indicate that pooling samples in microarray experiments where the biological variability is expected to be small might not be helpful and could even decrease one's ability to identify differentially expressed genes.