A wholly defined Agilent microarray spike-in dataset.

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However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms.\nRESULTS: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this 'Ag Spike' dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.\nAVAILABILITY: The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).", "claims": [{"id": "claim-target-result", "statement": "The study reports high agreement between Affymetrix and Agilent results and provides the Ag Spike raw data through the stated website and GEO accession GSE24866; the abstract does not name a specific statistical method.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:21414985", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms."}, {"asset": "source:pmid:21414985", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study reports high agreement between Affymetrix and Agilent results and provides the Ag Spike raw data through the stated website and GEO accession GSE24866; the abstract does not name a specific statistical method.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:21414985"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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Our previous wholly def", ", have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in wh", "agreement between results obtained using the Affymetrix and Agilent platforms. AVAILABILITY: The Ag"], "order_basis": "paper_text_order:0", "id": "assay:1"}]}