Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.
Microarray technology is a commonly used tool for assessing global gene expression. Many models for estimation of target concentration based on observed microarray signal have been proposed, but, in general, these models have been complex and platform-dependent.We introduce a universal Langmuir mode...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-12-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3012684?pdf=render |
| _version_ | 1819239396519444480 |
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| author | Raad Z Gharaibeh Anthony A Fodor Cynthia J Gibas |
| author_facet | Raad Z Gharaibeh Anthony A Fodor Cynthia J Gibas |
| author_sort | Raad Z Gharaibeh |
| collection | DOAJ |
| description | Microarray technology is a commonly used tool for assessing global gene expression. Many models for estimation of target concentration based on observed microarray signal have been proposed, but, in general, these models have been complex and platform-dependent.We introduce a universal Langmuir model for estimation of absolute target concentration from microarray experiments. We find that this sequence-independent model, characterized by only three free parameters, yields excellent predictions for four microarray platforms, including Affymetrix, Agilent, Illumina and a custom-printed microarray. The model also accurately predicts concentration for the MAQC data sets. This approach significantly reduces the computational complexity of quantitative target concentration estimates.Using a simple form of the Langmuir isotherm model, with a minimum of parameters and assumptions, and without explicit modeling of individual probe properties, we were able to recover absolute transcript concentrations with high R(2) on four different array platforms. The results obtained here suggest that with a "spiked-in" concentration series targeting as few as 5-10 genes, reliable estimation of target concentration can be achieved for the entire microarray. |
| first_indexed | 2024-12-23T13:51:27Z |
| format | Article |
| id | doaj.art-cabc04960f7b457db35b8a62016184f2 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T13:51:27Z |
| publishDate | 2010-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-cabc04960f7b457db35b8a62016184f22022-12-21T17:44:36ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-12-01512e1446410.1371/journal.pone.0014464Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.Raad Z GharaibehAnthony A FodorCynthia J GibasMicroarray technology is a commonly used tool for assessing global gene expression. Many models for estimation of target concentration based on observed microarray signal have been proposed, but, in general, these models have been complex and platform-dependent.We introduce a universal Langmuir model for estimation of absolute target concentration from microarray experiments. We find that this sequence-independent model, characterized by only three free parameters, yields excellent predictions for four microarray platforms, including Affymetrix, Agilent, Illumina and a custom-printed microarray. The model also accurately predicts concentration for the MAQC data sets. This approach significantly reduces the computational complexity of quantitative target concentration estimates.Using a simple form of the Langmuir isotherm model, with a minimum of parameters and assumptions, and without explicit modeling of individual probe properties, we were able to recover absolute transcript concentrations with high R(2) on four different array platforms. The results obtained here suggest that with a "spiked-in" concentration series targeting as few as 5-10 genes, reliable estimation of target concentration can be achieved for the entire microarray.http://europepmc.org/articles/PMC3012684?pdf=render |
| spellingShingle | Raad Z Gharaibeh Anthony A Fodor Cynthia J Gibas Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. PLoS ONE |
| title | Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. |
| title_full | Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. |
| title_fullStr | Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. |
| title_full_unstemmed | Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. |
| title_short | Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. |
| title_sort | accurate estimates of microarray target concentration from a simple sequence independent langmuir model |
| url | http://europepmc.org/articles/PMC3012684?pdf=render |
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