title: Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.
abstract: BACKGROUND
  The most commonly utilized microarrays for mRNA profiling (Affymetrix) include 'probe sets' of a series of perfect match and mismatch probes (typically 22 oligonucleotides per probe set). There are an increasing number of reported 'probe set algorithms' that differ in their interpretation of a probe set to derive a single normalized 'signal' representative of expression of each mRNA. These algorithms are known to differ in accuracy and sensitivity, and optimization has been done using a small set of standardized control microarray data. We hypothesized that different mRNA profiling projects have varying sources and degrees of confounding noise, and that these should alter the choice of a specific probe set algorithm. Also, we hypothesized that use of the Microarray Suite (MAS) 5.0 probe set detection p-value as a weighting function would improve the performance of all probe set algorithms.
  
  
  RESULTS
  We built an interactive visual analysis software tool (HCE2W) to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Five probe set algorithms were studied with and without statistical weighting of probe sets using the MAS 5.0 probe set detection p-values. The signal-to-noise ratio optimization method was tested in two large novel microarray datasets with different levels of confounding noise, a 105 sample U133A human muscle biopsy dataset (11 groups: mutation-defined, extensive noise), and a 40 sample U74A inbred mouse lung dataset (8 groups: little noise). Performance was measured by the ability of the specific probe set algorithm, with and without detection p-value weighting, to cluster samples into the appropriate biological groups (unsupervised agglomerative clustering with F-measure values). Of the total random sampling analyses, 50% showed a highly statistically significant difference between probe set algorithms by ANOVA [F(4,10) > 14, p < 0.0001], with weighting by MAS 5.0 detection p-value showing significance in the mouse data by ANOVA [F(1,10) > 9, p < 0.013] and paired t-test [t(9) = -3.675, p = 0.005]. Probe set detection p-value weighting had the greatest positive effect on performance of dChip difference model, ProbeProfiler and RMA algorithms. Importantly, probe set algorithms did indeed perform differently depending on the specific project, most probably due to the degree of confounding noise. Our data indicate that significantly improved data analysis of mRNA profile projects can be achieved by optimizing the choice of probe set algorithm with the noise levels intrinsic to a project, with dChip difference model with MAS 5.0 detection p-value continuous weighting showing the best overall performance in both projects. Furthermore, both existing and newly developed probe set algorithms should incorporate a detection p-value weighting to improve performance.
  
  
  BACKGROUND
  The Hierarchical Clustering Explorer 2.0 is available at http://www.cs.umd.edu/hcil/hce/ Murine arrays (40 samples) are publicly available at the PEPR resource (http://microarray.cnmcresearch.org/pgadatatable.asp http://pepr.cnmcresearch.org Chen et al., 2004).
authors.affiliation: Research Center for Genetic Medicine, Children's National Medical Center, MD, USA.
authors.forename: Jinwook
authors.initials: J
authors.lastname: Seo
authors.forename: Marina
authors.initials: M
authors.lastname: Bakay
authors.forename: Yi-Wen
authors.initials: YW
authors.lastname: Chen
authors.forename: Sara
authors.initials: S
authors.lastname: Hilmer
authors.forename: Ben
authors.initials: B
authors.lastname: Shneiderman
authors.forename: Eric P
authors.initials: EP
authors.lastname: Hoffman
mesh_terms: D016000:Cluster Analysis; D017076:Computer-Aided Design; D004867:Equipment Design / Q000379:methods*; D019544:Equipment Failure Analysis / Q000379:methods; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013269:Stochastic Processes; D014584:User-Computer Interface
chemical_list: D015345:Oligonucleotide Probes