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 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.
Lusa
L
L
Department of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milan, Italy. lara.lusa@ifom-ieo-campus.it
Cappelletti
V
V
Gariboldi
M
M
Ferrario
C
C
De Cecco
L
L
Reid
J F
JF
Toffanin
S
S
Gallus
G
G
McShane
L M
LM
Daidone
M G
MG
Pierotti
M A
MA
D018931:Antineoplastic Agents, Hormonal / Q000494:pharmacology; D015415:Biomarkers; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007091:Image Processing, Computer-Assisted; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D017312:Toremifene / Q000494:pharmacology
D018931:Antineoplastic Agents, Hormonal; D015415:Biomarkers; D017312:Toremifene