A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data
<p>Abstract</p> <p>Background</p> <p>In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of error...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2005-05-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/6/77 |
| _version_ | 1811297561048252416 |
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| author | Albers Casper J den Hengst Chris D Larsen Rasmus Kramer Naomi E Karsens Harma A Baerends Richard JS de Jong Anne van Hijum Sacha AFT Kok Jan Kuipers Oscar P |
| author_facet | Albers Casper J den Hengst Chris D Larsen Rasmus Kramer Naomi E Karsens Harma A Baerends Richard JS de Jong Anne van Hijum Sacha AFT Kok Jan Kuipers Oscar P |
| author_sort | Albers Casper J |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.</p> <p>Results</p> <p>A number of validation experiments were performed on <it>Lactococcus lactis </it>IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance.</p> <p>Conclusion</p> <p>Even in cases where 90 % of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25 %. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.</p> |
| first_indexed | 2024-04-13T06:06:15Z |
| format | Article |
| id | doaj.art-9ce6fe45fa2a40bdb4e0597150a8040d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T06:06:15Z |
| publishDate | 2005-05-01 |
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| series | BMC Genomics |
| spelling | doaj.art-9ce6fe45fa2a40bdb4e0597150a8040d2022-12-22T02:59:14ZengBMCBMC Genomics1471-21642005-05-01617710.1186/1471-2164-6-77A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray dataAlbers Casper Jden Hengst Chris DLarsen RasmusKramer Naomi EKarsens Harma ABaerends Richard JSde Jong Annevan Hijum Sacha AFTKok JanKuipers Oscar P<p>Abstract</p> <p>Background</p> <p>In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.</p> <p>Results</p> <p>A number of validation experiments were performed on <it>Lactococcus lactis </it>IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance.</p> <p>Conclusion</p> <p>Even in cases where 90 % of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25 %. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.</p>http://www.biomedcentral.com/1471-2164/6/77 |
| spellingShingle | Albers Casper J den Hengst Chris D Larsen Rasmus Kramer Naomi E Karsens Harma A Baerends Richard JS de Jong Anne van Hijum Sacha AFT Kok Jan Kuipers Oscar P A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data BMC Genomics |
| title | A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data |
| title_full | A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data |
| title_fullStr | A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data |
| title_full_unstemmed | A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data |
| title_short | A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data |
| title_sort | generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of dna microarray data |
| url | http://www.biomedcentral.com/1471-2164/6/77 |
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