Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and I...
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| Veröffentlicht in: | Nucleic acids research 2005-01, Vol.33 (18), p.5914-5923 |
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| creator | Barnes, Michael Freudenberg, Johannes Thompson, Susan Aronow, Bruce Pavlidis, Paul |
| description | The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms. |
| doi_str_mv | 10.1093/nar/gki890 |
| format | Article |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adult Cluster Analysis Gene Expression Profiling - methods Humans Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Probes Reproducibility of Results |
| title | Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms |
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