"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
<p>Abstract</p> <p>Background:</p> <p>The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationship between the probe int...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2008-08-01
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| Series: | Algorithms for Molecular Biology |
| Online Access: | http://www.almob.org/content/3/1/12 |
| _version_ | 1818749729675149312 |
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| author | Preibisch Stephan Binder Hans |
| author_facet | Preibisch Stephan Binder Hans |
| author_sort | Preibisch Stephan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background:</p> <p>The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationship between the probe intensity and the specific transcript concentration in a complex environment of competing interactions, the estimation of the magnitude these effects and their correction using the intensity information of a given chip and, finally the development of practicable algorithms which judge the quality of a particular hybridization and estimate the expression degree from the intensity values.</p> <p>Results:</p> <p>We present the so-called hook-calibration method which co-processes the log-difference (delta) and -sum (sigma) of the perfect match (PM) and mismatch (MM) probe-intensities. The MM probes are utilized as an internal reference which is subjected to the same hybridization law as the PM, however with modified characteristics. After sequence-specific affinity correction the method fits the Langmuir-adsorption model to the smoothed delta-versus-sigma plot. The geometrical dimensions of this so-called hook-curve characterize the particular hybridization in terms of simple geometric parameters which provide information about the mean non-specific background intensity, the saturation value, the mean PM/MM-sensitivity gain and the fraction of absent probes. This graphical summary spans a metrics system for expression estimates in natural units such as the mean binding constants and the occupancy of the probe spots. The method is single-chip based, i.e. it separately uses the intensities for each selected chip.</p> <p>Conclusion:</p> <p>The hook-method corrects the raw intensities for the non-specific background hybridization in a sequence-specific manner, for the potential saturation of the probe-spots with bound transcripts and for the sequence-specific binding of specific transcripts. The obtained chip characteristics in combination with the sensitivity corrected probe-intensity values provide expression estimates scaled in natural units which are given by the binding constants of the particular hybridization.</p> |
| first_indexed | 2024-12-18T04:08:25Z |
| format | Article |
| id | doaj.art-676b35f2b57e45c98720b5c4f65da0bb |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-12-18T04:08:25Z |
| publishDate | 2008-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-676b35f2b57e45c98720b5c4f65da0bb2022-12-21T21:21:32ZengBMCAlgorithms for Molecular Biology1748-71882008-08-01311210.1186/1748-7188-3-12"Hook"-calibration of GeneChip-microarrays: Theory and algorithmPreibisch StephanBinder Hans<p>Abstract</p> <p>Background:</p> <p>The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationship between the probe intensity and the specific transcript concentration in a complex environment of competing interactions, the estimation of the magnitude these effects and their correction using the intensity information of a given chip and, finally the development of practicable algorithms which judge the quality of a particular hybridization and estimate the expression degree from the intensity values.</p> <p>Results:</p> <p>We present the so-called hook-calibration method which co-processes the log-difference (delta) and -sum (sigma) of the perfect match (PM) and mismatch (MM) probe-intensities. The MM probes are utilized as an internal reference which is subjected to the same hybridization law as the PM, however with modified characteristics. After sequence-specific affinity correction the method fits the Langmuir-adsorption model to the smoothed delta-versus-sigma plot. The geometrical dimensions of this so-called hook-curve characterize the particular hybridization in terms of simple geometric parameters which provide information about the mean non-specific background intensity, the saturation value, the mean PM/MM-sensitivity gain and the fraction of absent probes. This graphical summary spans a metrics system for expression estimates in natural units such as the mean binding constants and the occupancy of the probe spots. The method is single-chip based, i.e. it separately uses the intensities for each selected chip.</p> <p>Conclusion:</p> <p>The hook-method corrects the raw intensities for the non-specific background hybridization in a sequence-specific manner, for the potential saturation of the probe-spots with bound transcripts and for the sequence-specific binding of specific transcripts. The obtained chip characteristics in combination with the sensitivity corrected probe-intensity values provide expression estimates scaled in natural units which are given by the binding constants of the particular hybridization.</p>http://www.almob.org/content/3/1/12 |
| spellingShingle | Preibisch Stephan Binder Hans "Hook"-calibration of GeneChip-microarrays: Theory and algorithm Algorithms for Molecular Biology |
| title | "Hook"-calibration of GeneChip-microarrays: Theory and algorithm |
| title_full | "Hook"-calibration of GeneChip-microarrays: Theory and algorithm |
| title_fullStr | "Hook"-calibration of GeneChip-microarrays: Theory and algorithm |
| title_full_unstemmed | "Hook"-calibration of GeneChip-microarrays: Theory and algorithm |
| title_short | "Hook"-calibration of GeneChip-microarrays: Theory and algorithm |
| title_sort | hook calibration of genechip microarrays theory and algorithm |
| url | http://www.almob.org/content/3/1/12 |
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