Questioning the utility of pooling samples in microarray experiments with cell lines

We describe a microarray experiment using the MCF-7 breast cancer cell line in two different experimental condi- tions 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 be- tween treated and untreated cells was about three times greater than that found using pools. These findings indicate that pool- ing 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. (Int J Biol Markers 2006; 21: 67-73)