Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio
Large scale −omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most −omics datasets due to variations in sample preparation, batching, platform settings, personnel, and other expe...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Systems Biology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fsysb.2023.1092341/full |
| _version_ | 1797348948730445824 |
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| author | Eric B. Dammer Eric B. Dammer Nicholas T. Seyfried Nicholas T. Seyfried Nicholas T. Seyfried Erik C. B. Johnson Erik C. B. Johnson |
| author_facet | Eric B. Dammer Eric B. Dammer Nicholas T. Seyfried Nicholas T. Seyfried Nicholas T. Seyfried Erik C. B. Johnson Erik C. B. Johnson |
| author_sort | Eric B. Dammer |
| collection | DOAJ |
| description | Large scale −omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most −omics datasets due to variations in sample preparation, batching, platform settings, personnel, and other experimental procedures prevent useful analyses of such data without prior adjustment for these technical factors. Here, we demonstrate a tunable median polish of ratio (TAMPOR) approach for batch effect correction and agglomeration of multiple, multi-batch, site-specific cohorts into a single analyte abundance data matrix that is suitable for systems biology analyses. We illustrate the utility and versatility of TAMPOR through four distinct use cases where the method has been applied to different proteomic datasets, some of which contain a specific defect that must be addressed prior to analysis. We compare quality control metrics and sources of variance before and after application of TAMPOR to show that TAMPOR is effective at removing batch effects and other unwanted sources of variance in −omics data. We also show how TAMPOR can be used to harmonize −omics datasets even when the data are acquired using different analytical approaches. TAMPOR is a powerful and flexible approach for cleaning and harmonization of −omics data prior to downstream systems biology analysis. |
| first_indexed | 2024-03-08T12:13:31Z |
| format | Article |
| id | doaj.art-04d70e67843d42299e64ea6b4e5a49b5 |
| institution | Directory Open Access Journal |
| issn | 2674-0702 |
| language | English |
| last_indexed | 2024-03-08T12:13:31Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Systems Biology |
| spelling | doaj.art-04d70e67843d42299e64ea6b4e5a49b52024-01-22T17:25:47ZengFrontiers Media S.A.Frontiers in Systems Biology2674-07022023-04-01310.3389/fsysb.2023.10923411092341Batch correction and harmonization of –Omics datasets with a tunable median polish of ratioEric B. Dammer0Eric B. Dammer1Nicholas T. Seyfried2Nicholas T. Seyfried3Nicholas T. Seyfried4Erik C. B. Johnson5Erik C. B. Johnson6Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, United StatesDepartment of Biochemistry, Emory University School of Medicine, Atlanta, GA, United StatesGoizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, United StatesDepartment of Biochemistry, Emory University School of Medicine, Atlanta, GA, United StatesDepartment of Neurology, Emory University School of Medicine, Atlanta, GA, United StatesGoizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, United StatesDepartment of Neurology, Emory University School of Medicine, Atlanta, GA, United StatesLarge scale −omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most −omics datasets due to variations in sample preparation, batching, platform settings, personnel, and other experimental procedures prevent useful analyses of such data without prior adjustment for these technical factors. Here, we demonstrate a tunable median polish of ratio (TAMPOR) approach for batch effect correction and agglomeration of multiple, multi-batch, site-specific cohorts into a single analyte abundance data matrix that is suitable for systems biology analyses. We illustrate the utility and versatility of TAMPOR through four distinct use cases where the method has been applied to different proteomic datasets, some of which contain a specific defect that must be addressed prior to analysis. We compare quality control metrics and sources of variance before and after application of TAMPOR to show that TAMPOR is effective at removing batch effects and other unwanted sources of variance in −omics data. We also show how TAMPOR can be used to harmonize −omics datasets even when the data are acquired using different analytical approaches. TAMPOR is a powerful and flexible approach for cleaning and harmonization of −omics data prior to downstream systems biology analysis.https://www.frontiersin.org/articles/10.3389/fsysb.2023.1092341/fullbatch correctionmulti-platformmulti-cohortproteomicsmedian polishmulti-omics |
| spellingShingle | Eric B. Dammer Eric B. Dammer Nicholas T. Seyfried Nicholas T. Seyfried Nicholas T. Seyfried Erik C. B. Johnson Erik C. B. Johnson Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio Frontiers in Systems Biology batch correction multi-platform multi-cohort proteomics median polish multi-omics |
| title | Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio |
| title_full | Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio |
| title_fullStr | Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio |
| title_full_unstemmed | Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio |
| title_short | Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio |
| title_sort | batch correction and harmonization of omics datasets with a tunable median polish of ratio |
| topic | batch correction multi-platform multi-cohort proteomics median polish multi-omics |
| url | https://www.frontiersin.org/articles/10.3389/fsysb.2023.1092341/full |
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