PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization
| dc.contributor.author | Da Gama Duarte, Jessica | |
| dc.contributor.author | Goosen, Ryan W | |
| dc.contributor.author | Lawry, Peter J | |
| dc.contributor.author | Blackburn, Jonathan M | |
| dc.date.accessioned | 2018-05-07T09:03:24Z | |
| dc.date.available | 2018-05-07T09:03:24Z | |
| dc.date.issued | 2018-02-27 | |
| dc.date.updated | 2018-04-09T15:10:14Z | |
| dc.description.abstract | Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. | |
| dc.identifier.apacitation | Da Gama Duarte, J., Goosen, R. W., Lawry, P. J., & Blackburn, J. M. (2018). PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. <i>BMC Res Notes</i>, http://hdl.handle.net/11427/27938 | en_ZA |
| dc.identifier.chicagocitation | Da Gama Duarte, Jessica, Ryan W Goosen, Peter J Lawry, and Jonathan M Blackburn "PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization." <i>BMC Res Notes</i> (2018) http://hdl.handle.net/11427/27938 | en_ZA |
| dc.identifier.citation | Duarte, J. D. G., Goosen, R. W., Lawry, P. J., & Blackburn, J. M. (2018). PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC research notes, 11(1), 156. | |
| dc.identifier.ris | TY - Journal Article AU - Da Gama Duarte, Jessica AU - Goosen, Ryan W AU - Lawry, Peter J AU - Blackburn, Jonathan M AB - Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. DA - 2018-02-27 DB - OpenUCT DO - 10.1186/s13104-018-3266-0 DP - University of Cape Town J1 - BMC Res Notes LK - https://open.uct.ac.za PB - University of Cape Town PY - 2018 T1 - PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization TI - PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization UR - http://hdl.handle.net/11427/27938 ER - | en_ZA |
| dc.identifier.uri | http://dx.doi.org/10.1186/s13104-018-3266-0 | |
| dc.identifier.uri | http://hdl.handle.net/11427/27938 | |
| dc.identifier.vancouvercitation | Da Gama Duarte J, Goosen RW, Lawry PJ, Blackburn JM. PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC Res Notes. 2018; http://hdl.handle.net/11427/27938. | en_ZA |
| dc.language.iso | en | |
| dc.publisher | BioMed Central | |
| dc.publisher.department | Institute of Infectious Disease and Molecular Medicine | en_ZA |
| dc.publisher.faculty | Faculty of Health Sciences | en_ZA |
| dc.publisher.institution | University of Cape Town | |
| dc.rights.holder | The Author(s) | |
| dc.source | BMC Res Notes | |
| dc.source.uri | https://bmcresnotes.biomedcentral.com/ | |
| dc.subject.other | Protein microarrays | |
| dc.subject.other | Protein Microarray Analyser | |
| dc.subject.other | PMA | |
| dc.title | PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization | |
| dc.type | Journal Article | |
| uct.type.filetype | Text | |
| uct.type.filetype | Image |