Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing.

ABSTRACT: Due to the great variety of preprocessing tools in two-channel expression microarray data analysis it is difficult to choose the most appropriate one for a given experimental setup. In our study, two independent two-channel inhouse microarray experiments as well as a publicly available dataset were used to investigate the influence of the selection of preprocessing methods (background correction, normalization, and duplicate spots correlation calculation) on the discovery of differentially expressed genes. Here we are showing that both the list of differentially expressed genes and the expression values of selected genes depend significantly on the preprocessing approach applied. The choice of normalization method to be used had the highest impact on the results. We propose a simple but ef

SUBMITTER: Rotter A 

PROVIDER: S-EPMC3184524 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature