Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
<p>Abstract</p> <p>Background</p> <p>Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the...
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| Format: | Article |
| Language: | English |
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BMC
2010-05-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/285 |
| _version_ | 1811331088889413632 |
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| author | Zhu Qianqian Miecznikowski Jeffrey C Halfon Marc S |
| author_facet | Zhu Qianqian Miecznikowski Jeffrey C Halfon Marc S |
| author_sort | Zhu Qianqian |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.</p> <p>Results</p> <p>We generated a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive versus negative fold change. We use this new "Platinum Spike" dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.</p> <p>Conclusions</p> <p>We present updated best-route methods for Affymetrix GeneChip analysis and demonstrate that the degree of "imbalance" in gene expression has a significant effect on the performance of these methods.</p> |
| first_indexed | 2024-04-13T16:13:37Z |
| format | Article |
| id | doaj.art-53c549097da14c3dbe86cddbd3551db8 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T16:13:37Z |
| publishDate | 2010-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-53c549097da14c3dbe86cddbd3551db82022-12-22T02:40:08ZengBMCBMC Bioinformatics1471-21052010-05-0111128510.1186/1471-2105-11-285Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in datasetZhu QianqianMiecznikowski Jeffrey CHalfon Marc S<p>Abstract</p> <p>Background</p> <p>Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.</p> <p>Results</p> <p>We generated a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive versus negative fold change. We use this new "Platinum Spike" dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.</p> <p>Conclusions</p> <p>We present updated best-route methods for Affymetrix GeneChip analysis and demonstrate that the degree of "imbalance" in gene expression has a significant effect on the performance of these methods.</p>http://www.biomedcentral.com/1471-2105/11/285 |
| spellingShingle | Zhu Qianqian Miecznikowski Jeffrey C Halfon Marc S Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset BMC Bioinformatics |
| title | Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset |
| title_full | Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset |
| title_fullStr | Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset |
| title_full_unstemmed | Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset |
| title_short | Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset |
| title_sort | preferred analysis methods for affymetrix genechips ii an expanded balanced wholly defined spike in dataset |
| url | http://www.biomedcentral.com/1471-2105/11/285 |
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