Diagnostic robustness of DNA microarrays in the classification of acute leukemia

Adrian Mondry — Wed, 26 Sep 2007 05:03:33 UTC

Countless statistical methods have been described for the analysis of DNA microarrays, and each yields distinct results. This raises the question whether DNA microarrays are robust diagnostic tools.In order to address this issue, we compared five formally similar statistical tests for gene selection on a single data set derived from acute leukemia patients. Inter-test agreement of gene selection, of sample classification and with standard clinical diagnosis was calculated using Cohen’s κ-score.The inter-test agreement scores were 0.15 < κ < 0.68 for gene selection, and 0.60 < κ < 0.89 for sample classification. Comparison to the clinical diagnosis showed agreement scores of 0.58< κ < 0.88. ‘Marginal imbalance’ explains the low κ-scores at the level of gene selection. At the levels of sample classification and agreement with clinical diagnosis, κ-scores can be considered “substantial” to “excellent”.For diagnostic purposes, the inter-test agreement of DNA microarrays is equivalent to that of experienced clinicians, as reported in the literature. The technique can thus be considered a useful and robust addendum to the available diagnostic tools.

DNA expression microarrays may be the wrong tool to identify biological pathways

Adrian Mondry — Wed, 19 Sep 2007 17:07:01 UTC

DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen’s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 < k < 0.79) between the analysis methods used. Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used.

Nature Precedings - Adrian Mondry

Diagnostic robustness of DNA microarrays in the classification of acute leukemia

DNA expression microarrays may be the wrong tool to identify biological pathways