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

L Lusa; V Cappelletti; M Gariboldi; C Ferrario; L De Cecco; J F Reid; S Toffanin; G Gallus; L M McShane; M G Daidone; M A Pierotti

doi:10.1177/172460080602100201

PubMed · 16847808

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

L Lusa·V Cappelletti·M Gariboldi·C Ferrario·L De Cecco·J F Reid·S Toffanin·G Gallus·L M McShane·M G Daidone·M A Pierotti

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Abstract

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.

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Antineoplastic Agents, Hormonal Biomarkers Breast Neoplasms Cell Line, Tumor Computational Biology Gene Expression Profiling Gene Expression Regulation, Neoplastic Humans Image Processing, Computer-Assisted Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Quality Control Toremifene Journal Article Research Support, Non-U.S. Gov't

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L Lusa, V Cappelletti, M Gariboldi, C Ferrario, L De Cecco, J F Reid, S Toffanin, G Gallus, L M McShane, M G Daidone, M A Pierotti. Questioning the utility of pooling samples in microarray experiments with cell lines.. https://doi.org/10.1177/172460080602100201

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