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2011-08-04Zeitschriftenartikel DOI: 10.1186/1471-2105-12-324
rapmad: Robust analysis of peptide microarray data
dc.contributor.authorRenard, Bernhard Y.
dc.contributor.authorLöwer, Martin
dc.contributor.authorKühne, Yvonne
dc.contributor.authorReimer, Ulf
dc.contributor.authorRothermel, Andrée
dc.contributor.authorTüreci, Özlem
dc.contributor.authorCastle, John C.
dc.contributor.authorSahin, Ugur
dc.date.accessioned2018-05-07T14:49:09Z
dc.date.available2018-05-07T14:49:09Z
dc.date.created2011-09-19
dc.date.issued2011-08-04none
dc.identifier.otherhttp://edoc.rki.de/oa/articles/reEZgqdXPsdrk/PDF/26zO0OSyhwU0c.pdf
dc.identifier.urihttp://edoc.rki.de/176904/944
dc.description.abstractBackground: Peptide microarrays offer an enormous potential as a screening tool for peptidomics experiments and have recently seen an increased field of application ranging from immunological studies to systems biology. By allowing the parallel analysis of thousands of peptides in a single run they are suitable for high-throughput settings. Since data characteristics of peptide microarrays differ from DNA oligonucleotide microarrays, computational methods need to be tailored to these specifications to allow a robust and automated data analysis. While follow-up experiments can ensure the specificity of results, sensitivity cannot be recovered in later steps. Providing sensitivity is thus a primary goal of data analysis procedures. To this end we created rapmad (Robust Alignment of Peptide MicroArray Data), a novel computational tool implemented in R. Results: We evaluated rapmad in antibody reactivity experiments for several thousand peptide spots and compared it to two existing algorithms for the analysis of peptide microarrays. rapmad displays competitive and superior behavior to existing software solutions. Particularly, it shows substantially improved sensitivity for low intensity settings without sacrificing specificity. It thereby contributes to increasing the effectiveness of high throughput screening experiments. Conclusions: rapmad allows the robust and sensitive, automated analysis of high-throughput peptide array data. The rapmad R-package as well as the data sets are available from http://www.tron-mz.de/compmed.eng
dc.language.isoeng
dc.publisherRobert Koch-Institut
dc.subjectHumanseng
dc.subjectSensitivity and Specificityeng
dc.subjectAlgorithmseng
dc.subjectNeoplasms/metabolismeng
dc.subjectProtein Array Analysis/methodseng
dc.subjectSoftwareeng
dc.subjectTumor Markers Biological*eng
dc.subject.ddc610 Medizin
dc.titlerapmad: Robust analysis of peptide microarray data
dc.typeperiodicalPart
dc.identifier.urnurn:nbn:de:0257-10015365
dc.identifier.doi10.1186/1471-2105-12-324
dc.identifier.doihttp://dx.doi.org/10.25646/869
local.edoc.container-titleBMC Bioinformatics
local.edoc.fp-subtypeArtikel
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttp://www.biomedcentral.com/1471-2105/12/324
local.edoc.container-publisher-nameBioMedCentral
local.edoc.container-volume12
local.edoc.container-issue324
local.edoc.container-year2011

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