Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples.

ABSTRACT:

Background

Several preprocessing algorithms for Affymetrix gene expression microarrays have been developed, and their performance on spike-in data sets has been evaluated previously. However, a comprehensive comparison of preprocessing algorithms on samples taken under research conditions has not been performed.

Methodology/principal findings

We used TaqMan RT-PCR arrays as a reference to evaluate the accuracy of expression values from Affymetrix microarrays in two experimental data sets: one comprising 84 genes in 36 colon biopsies, and the other comprising 75 genes in 29 cancer cell lines. We evaluated consistency using the Pearson correlation between measurements obtained on the two platforms. Also, we introduce the log-ratio discrepancy as a more relevant measure of disc

SUBMITTER: Gyorffy B 

PROVIDER: S-EPMC2680989 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature