{
  "@type": "dcat:Dataset",
  "accessLevel": "public",
  "bureauCode": [
    "009:25"
  ],
  "contactPoint": {
    "@type": "vcard:Contact",
    "fn": "NIH",
    "hasEmail": "mailto:info@nih.gov"
  },
  "description": "Background\n          A model-based analysis of oligonucleotide expression arrays we developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes (MBEI). MBEI has standard error attached to it as a measure of accuracy. Here we investigate the stability of the probe-sensitivity index across different tissue types, the reproducibility of results in replicate experiments, and the use of MBEI in perfect match (PM)-only arrays.\n        \n        \n          Results\n          Probe-sensitivity indexes are stable across tissue types. The target gene's presence in many arrays of an array set allows the probe-sensitivity index to be estimated accurately. We extended the model to obtain expression values for PM-only arrays, and found that the 20-probe PM-only model is comparable to the 10-probe PM/MM difference model, in terms of the expression correlations with the original 20-probe PM/MM difference model. MBEI method is able to extend the reliable detection limit of expression to a lower mRNA concentration. The standard errors of MBEI can be used to construct confidence intervals of fold changes, and the lower confidence bound of fold change is a better ranking statistic for filtering genes. We can assign reliability indexes for genes in a specific cluster of interest in hierarchical clustering by resampling clustering trees. A software dChip implementing many of these analysis methods is made available.\n        \n        \n          Conclusions\n          The model-based approach reduces the variability of low expression estimates, and provides a natural method of calculating expression values for PM-only arrays. The standard errors attached to expression values can be used to assess the reliability of downstream analysis.",
  "distribution": [
    {
      "@type": "dcat:Distribution",
      "description": "Visit the original government dataset for complete information, documentation, and data access.",
      "downloadURL": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC55329/",
      "mediaType": "text/html",
      "title": "Official Government Data Source"
    }
  ],
  "identifier": "https://healthdata.gov/api/views/prtx-u7ym",
  "issued": "2025-07-14",
  "keyword": [
    "gene-expression",
    "microarray-analysis",
    "nih",
    "oligonucleotide-arrays",
    "probe-sensitivity"
  ],
  "landingPage": "https://healthdata.gov/d/prtx-u7ym",
  "modified": "2025-09-06",
  "programCode": [
    "009:033"
  ],
  "publisher": {
    "@type": "org:Organization",
    "name": "National Institutes of Health"
  },
  "theme": [
    "NIH"
  ],
  "title": "Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application"
}