{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T18:15:09Z","timestamp":1763662509551,"version":"3.30.2"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Gene expression index calculations from Affymetrix GeneChips have been dominated by the Affymetrix MAS, dChip, and RMA methods. A new method to estimate the gene expression value utilizing the probe sequence information named position-dependent nearest-neighbor (PDNN) has been suggested by Zhang et al. (2003). Here we describe an open source implementation of the PDNN method for the statistical language R.<\/jats:p><jats:p>Availability: The package can be downloaded from http:\/\/www.bioconductor.org\/repository\/devel\/package\/html\/affypdnn.html<\/jats:p><jats:p>Contact: \u00a0hbjorn@cbs.dtu.dk<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti078","type":"journal-article","created":{"date-parts":[[2004,10,28]],"date-time":"2004-10-28T00:23:01Z","timestamp":1098922981000},"page":"687-688","source":"Crossref","is-referenced-by-count":9,"title":["Implementation of a gene expression index calculation method based on the PDNN model"],"prefix":"10.1093","volume":"21","author":[{"given":"Henrik Bj\u00f8rn","family":"Nielsen","sequence":"first","affiliation":[{"name":"Center for Biological Sequence Analysis, BioCentrum-DTU Technical University of Denmark Building 208, DK-2800 Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurent","family":"Gautier","sequence":"additional","affiliation":[{"name":"Center for Biological Sequence Analysis, BioCentrum-DTU Technical University of Denmark Building 208, DK-2800 Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steen","family":"Knudsen","sequence":"additional","affiliation":[{"name":"Center for Biological Sequence Analysis, BioCentrum-DTU Technical University of Denmark Building 208, DK-2800 Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,10,27]]},"reference":[{"key":"2023013107223530300_B1","doi-asserted-by":"crossref","unstructured":"Li, C. and Wong, W.H. 2001Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol.2RESEARCH0032","DOI":"10.1186\/gb-2001-2-8-research0032"},{"key":"2023013107223530300_B2","doi-asserted-by":"crossref","unstructured":"Gautier, L., Cope, L., Bolstad, B.M., Irizarry, R.A. 2004Affy\u2014analysis of Affymetrix GeneChip data at the probe level. Bioinformatics20307\u2013315","DOI":"10.1093\/bioinformatics\/btg405"},{"key":"2023013107223530300_B3","unstructured":"Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., Speed, T.P. 2003Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics2249\u2013264"},{"key":"2023013107223530300_B4","doi-asserted-by":"crossref","unstructured":"Zhang, L., Miles, M.F., Aldape, K.D. 2003A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol.7818\u2013821","DOI":"10.1038\/nbt836"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/5\/687\/48962429\/bioinformatics_21_5_687.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/5\/687\/48962429\/bioinformatics_21_5_687.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T05:31:21Z","timestamp":1734586281000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/5\/687\/220375"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,10,27]]},"references-count":4,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2005,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti078","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2005,3,1]]},"published":{"date-parts":[[2004,10,27]]}}}