Hematologic Malignancies, Molecular Oncology and Clinical Investigations Programs, Department of Interdisciplinary Oncology Program, H, Lee Moffitt Cancer Center and Research Institute. kothapar@moffitt.usf.edu
BACKGROUND: DNA microarray technology is a powerful technique that was recently developed in order to analyze thousands of genes in a short time. Presently, microarrays, or chips, of the cDNA type and oligonucleotide type are available from several sources. The number of publications in this area is increasing exponentially. RESULTS: In this study, microarray data obtained from two different commercially available systems were critically evaluated. Our analysis revealed several inconsistencies in the data obtained from the two different microarrays. Problems encountered included inconsistent sequence fidelity of the spotted microarrays, variability of differential expression, low specificity of cDNA microarray probes, discrepancy in fold-change calculation and lack of probe specificity for different isoforms of a gene. CONCLUSIONS: In view of these pitfalls, data from microarray analysis need to be interpreted cautiously.