Exploring the use of internal and externalcontrols for assessing microarray technical performance
<p>Abstract</p> <p>Background</p> <p>The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospect...
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| Format: | Article |
| Language: | English |
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BMC
2010-12-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/3/349 |
| _version_ | 1828530062618525696 |
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| author | Game Laurence Salit Marc L Duewer David L Lippa Katrice A Causton Helen C |
| author_facet | Game Laurence Salit Marc L Duewer David L Lippa Katrice A Causton Helen C |
| author_sort | Game Laurence |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies.</p> <p>Results</p> <p>A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics.</p> <p>Conclusions</p> <p>These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.</p> |
| first_indexed | 2024-12-11T22:17:48Z |
| format | Article |
| id | doaj.art-25fb3e8568124495bf34b27a20c17840 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-11T22:17:48Z |
| publishDate | 2010-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-25fb3e8568124495bf34b27a20c178402022-12-22T00:48:33ZengBMCBMC Research Notes1756-05002010-12-013134910.1186/1756-0500-3-349Exploring the use of internal and externalcontrols for assessing microarray technical performanceGame LaurenceSalit Marc LDuewer David LLippa Katrice ACauston Helen C<p>Abstract</p> <p>Background</p> <p>The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies.</p> <p>Results</p> <p>A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics.</p> <p>Conclusions</p> <p>These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.</p>http://www.biomedcentral.com/1756-0500/3/349 |
| spellingShingle | Game Laurence Salit Marc L Duewer David L Lippa Katrice A Causton Helen C Exploring the use of internal and externalcontrols for assessing microarray technical performance BMC Research Notes |
| title | Exploring the use of internal and externalcontrols for assessing microarray technical performance |
| title_full | Exploring the use of internal and externalcontrols for assessing microarray technical performance |
| title_fullStr | Exploring the use of internal and externalcontrols for assessing microarray technical performance |
| title_full_unstemmed | Exploring the use of internal and externalcontrols for assessing microarray technical performance |
| title_short | Exploring the use of internal and externalcontrols for assessing microarray technical performance |
| title_sort | exploring the use of internal and externalcontrols for assessing microarray technical performance |
| url | http://www.biomedcentral.com/1756-0500/3/349 |
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