Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data
<p>Abstract</p> <p>Background</p> <p>There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-08-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/334 |
| _version_ | 1818157804495568896 |
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| author | Pocock Matthew R Oinn Tom Withers David Owen Stuart Soiland-Reyes Stian Wassink Ingo Velarde Giles Castrillo Juan I Li Peter Goble Carole A Oliver Stephen G Kell Douglas B |
| author_facet | Pocock Matthew R Oinn Tom Withers David Owen Stuart Soiland-Reyes Stian Wassink Ingo Velarde Giles Castrillo Juan I Li Peter Goble Carole A Oliver Stephen G Kell Douglas B |
| author_sort | Pocock Matthew R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools.</p> <p>Results</p> <p>Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and <it>ad hoc </it>analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench.</p> <p>Conclusion</p> <p>Taverna can be used by data analysis experts as a generic tool for composing <it>ad hoc </it>analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.</p> |
| first_indexed | 2024-12-11T15:20:01Z |
| format | Article |
| id | doaj.art-6e34f5835e0a41c7b7d54e834d4fd72b |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T15:20:01Z |
| publishDate | 2008-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-6e34f5835e0a41c7b7d54e834d4fd72b2022-12-22T01:00:25ZengBMCBMC Bioinformatics1471-21052008-08-019133410.1186/1471-2105-9-334Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray dataPocock Matthew ROinn TomWithers DavidOwen StuartSoiland-Reyes StianWassink IngoVelarde GilesCastrillo Juan ILi PeterGoble Carole AOliver Stephen GKell Douglas B<p>Abstract</p> <p>Background</p> <p>There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools.</p> <p>Results</p> <p>Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and <it>ad hoc </it>analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench.</p> <p>Conclusion</p> <p>Taverna can be used by data analysis experts as a generic tool for composing <it>ad hoc </it>analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.</p>http://www.biomedcentral.com/1471-2105/9/334 |
| spellingShingle | Pocock Matthew R Oinn Tom Withers David Owen Stuart Soiland-Reyes Stian Wassink Ingo Velarde Giles Castrillo Juan I Li Peter Goble Carole A Oliver Stephen G Kell Douglas B Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data BMC Bioinformatics |
| title | Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data |
| title_full | Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data |
| title_fullStr | Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data |
| title_full_unstemmed | Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data |
| title_short | Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data |
| title_sort | performing statistical analyses on quantitative data in taverna workflows an example using r and maxdbrowse to identify differentially expressed genes from microarray data |
| url | http://www.biomedcentral.com/1471-2105/9/334 |
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