A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data
<p>Abstract</p> <p>Background</p> <p>Affymetrix GeneChip typically contains multiple probe sets per gene, defined as sibling probe sets in this study. These probe sets may or may not behave similar across treatments. The most appropriate way of consolidating sibling pro...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-04-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/188 |
| _version_ | 1819087726908014592 |
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| author | Zhu Dongxiao Li Hua Cook Malcolm |
| author_facet | Zhu Dongxiao Li Hua Cook Malcolm |
| author_sort | Zhu Dongxiao |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Affymetrix GeneChip typically contains multiple probe sets per gene, defined as sibling probe sets in this study. These probe sets may or may not behave similar across treatments. The most appropriate way of consolidating sibling probe sets suitable for analysis is an open problem. We propose the Analysis of Variance (ANOVA) framework to decide which sibling probe sets can be consolidated.</p> <p>Results</p> <p>The ANOVA model allows us to separate the sibling probe sets into two types: those behave similarly across treatments and those behave differently across treatments. We found that consolidation of sibling probe sets of the former type results in large increase in the number of differentially expressed genes under various statistical criteria. The approach to selecting sibling probe sets suitable for consolidating is implemented in R language and freely available from <url>http://research.stowers-institute.org/hul/affy/</url>.</p> <p>Conclusion</p> <p>Our ANOVA analysis of sibling probe sets provides a statistical framework for selecting sibling probe sets for consolidation. Consolidating sibling probe sets by pooling data from each greatly improves the estimates of a gene expression level and results in identification of more biologically relevant genes. Sibling probe sets that do not qualify for consolidation may represent annotation errors or other artifacts, or may correspond to differentially processed transcripts of the same gene that require further analysis.</p> |
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| format | Article |
| id | doaj.art-af18a2b279524bbeb6d767758adf134b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T21:40:44Z |
| publishDate | 2008-04-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-af18a2b279524bbeb6d767758adf134b2022-12-21T18:49:21ZengBMCBMC Genomics1471-21642008-04-019118810.1186/1471-2164-9-188A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip dataZhu DongxiaoLi HuaCook Malcolm<p>Abstract</p> <p>Background</p> <p>Affymetrix GeneChip typically contains multiple probe sets per gene, defined as sibling probe sets in this study. These probe sets may or may not behave similar across treatments. The most appropriate way of consolidating sibling probe sets suitable for analysis is an open problem. We propose the Analysis of Variance (ANOVA) framework to decide which sibling probe sets can be consolidated.</p> <p>Results</p> <p>The ANOVA model allows us to separate the sibling probe sets into two types: those behave similarly across treatments and those behave differently across treatments. We found that consolidation of sibling probe sets of the former type results in large increase in the number of differentially expressed genes under various statistical criteria. The approach to selecting sibling probe sets suitable for consolidating is implemented in R language and freely available from <url>http://research.stowers-institute.org/hul/affy/</url>.</p> <p>Conclusion</p> <p>Our ANOVA analysis of sibling probe sets provides a statistical framework for selecting sibling probe sets for consolidation. Consolidating sibling probe sets by pooling data from each greatly improves the estimates of a gene expression level and results in identification of more biologically relevant genes. Sibling probe sets that do not qualify for consolidation may represent annotation errors or other artifacts, or may correspond to differentially processed transcripts of the same gene that require further analysis.</p>http://www.biomedcentral.com/1471-2164/9/188 |
| spellingShingle | Zhu Dongxiao Li Hua Cook Malcolm A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data BMC Genomics |
| title | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| title_full | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| title_fullStr | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| title_full_unstemmed | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| title_short | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| title_sort | statistical framework for consolidating sibling probe sets for affymetrix genechip data |
| url | http://www.biomedcentral.com/1471-2164/9/188 |
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