Recovery of biological information under heterogeneous experimental conditions using subgroup standardization.. Homo sapiens

Recovery of biological information (i.e. Breast tumor versus non-tumor part of breast) from microarray data under heterogeneous experimental conditions (Buffer1 versus Buffer2) using subgroup standardization. Microarray is a useful tool for gene expression analysis and prediction. For a given disease, a microarray database may come from various sources with different experimental setups, collected over time. This heterogeneity provides unnecessary complication in data analysis and, even worse, given false classification in clustering. Therefore, it is practically important to provide a standard data treatment for microarray data from heterogeneous experimental conditions. In this work, “subgroup standardization” is proposed to compensate technical heterogeneities (e.g., buffers, time, machines etc.) in microarray experimental conditions. Provided with repetitive microarray experiments, over time and buffers, the results indicate that the proposed approach can extract correct biological information in the presence of technical irregularities. Hierarchical clustering is used to validate the effectiveness of the proposed approach. Keywords: disease state study Overall design: 98 of breast cancer specimens and 8 of non-tumor part of breast specimens were applied in the study. All the signals from the mRNA profile of each sample in the microarrays were normalized using the internal control RNA- Stratagene's human common reference RNA.