title: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Hungarian Academy of Sciences and Semmelweis University Budapest, Budapest, Hungary.
authors.forename: Balazs
authors.initials: B
authors.lastname: Gyorffy
authors.forename: Bela
authors.initials: B
authors.lastname: Molnar
authors.forename: Hermann
authors.initials: H
authors.lastname: Lage
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Szallasi
authors.forename: Aron C
authors.initials: AC
authors.lastname: Eklund
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D030561:Databases, Nucleic Acid; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction