Dataset Information

Improving the default data analysis workflow for large autoimmune biomarker discovery studies with ProtoArrays.

ABSTRACT: Contemporary protein microarrays such as the ProtoArray® are used for autoimmune antibody screening studies to discover biomarker panels. For ProtoArray data analysis, the software Prospector and a default workflow are suggested by the manufacturer. While analyzing a large data set of a discovery study for diagnostic biomarkers of the Parkinson's disease (ParkCHIP), we have revealed the need for distinct improvements of the suggested workflow concerning raw data acquisition, normalization and preselection method availability, batch effects, feature selection, and feature validation. In this work, appropriate improvements of the default workflow are proposed. It is shown that completely automatic data acquisition as a batch, a re-implementation of Prospector's pre-selection method, multivariate or hybrid feature selection, and validation of the selected protein panel using an independent test set define in combination an improved workflow for large studies.

SUBMITTER: Turewicz M

PROVIDER: S-EPMC3810711 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Improving the default data analysis workflow for large autoimmune biomarker discovery studies with ProtoArrays.

Turewicz Michael M May Caroline C Ahrens Maike M Woitalla Dirk D Gold Ralf R Casjens Swaantje S Pesch Beate B Brüning Thomas T Meyer Helmut E HE Nordhoff Eckhard E Böckmann Miriam M Stephan Christian C Eisenacher Martin M

Proteomics 20130620 14

Contemporary protein microarrays such as the ProtoArray® are used for autoimmune antibody screening studies to discover biomarker panels. For ProtoArray data analysis, the software Prospector and a default workflow are suggested by the manufacturer. While analyzing a large data set of a discovery study for diagnostic biomarkers of the Parkinson's disease (ParkCHIP), we have revealed the need for distinct improvements of the suggested workflow concerning raw data acquisition, normalization and pr ...[more]

PMID: 23616427

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Dataset Information

Improving the default data analysis workflow for large autoimmune biomarker discovery studies with ProtoArrays.

Publications

Improving the default data analysis workflow for large autoimmune biomarker discovery studies with ProtoArrays.

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