Article thumbnail

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

By Balázs Győrffy, Béla Ákos Molnár, Hermann Lage, Zoltán Szállási and Aron C Eklund

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 discordance between gene expression platforms. Of nine preprocessing algorithms tested, PLIER+16 produced expression values that were most consistent with RT-PCR measurements, although the difference in performance between most of the algorithms was not statistically significant. CONCLUSIONS/SIGNIFICANCE Our results support the choice of PLIER+16 for the preprocessing of clinical Affymetrix microarray data. However, other algorithms performed similarly and are probably also good choices

Topics: R1 Medicine (General) / orvostudomány általában
Publisher: 'Public Library of Science (PLoS)'
Year: 2009
DOI identifier: 10.1371/journal.pone.0005645
OAI identifier: oai:real.mtak.hu:55977

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles