{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:36:01Z","timestamp":1761237361309},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,1]]},"abstract":"Abstract<\/jats:title>\n Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative processing procedure that comprises five major functional components, namely the raw microarray data parsing and integrating module, the array spatial effect smoothing and visualization module, the probe-level multi-array normalization module, the gene expression intensity summarization module and the gene expression status inference module.<\/jats:p>\n Availability: \u00a0<\/jats:p>\n Contact: \u00a0Xiangfeng.Wang@Yale.edu<\/jats:p>\n Supplementary information: The supplementary materials, figures, testing dataset, software instructions and a typical workflow of using NMPP package are accessible through the above homepage.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl525","type":"journal-article","created":{"date-parts":[[2006,10,13]],"date-time":"2006-10-13T07:47:15Z","timestamp":1160725635000},"page":"2955-2957","source":"Crossref","is-referenced-by-count":25,"title":["NMPP: a user-customized NimbleGen microarray data processing pipeline"],"prefix":"10.1093","volume":"22","author":[{"given":"Xiangfeng","family":"Wang","sequence":"first","affiliation":[{"name":"Center of Bioinformatics & Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University 1 \u00a0 1 \u00a0 \u00a0 Beijing 100871, China"},{"name":"Department of Molecular, Cellular, and Developmental Biology, Yale University 2 \u00a0 2 \u00a0 \u00a0 New Haven, CT 06520, USA"}]},{"given":"Hang","family":"He","sequence":"additional","affiliation":[{"name":"Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences 3 \u00a0 3 \u00a0 \u00a0 Beijing 100101, China"}]},{"given":"Lei","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular, and Developmental Biology, Yale University 2 \u00a0 2 \u00a0 \u00a0 New Haven, CT 06520, USA"}]},{"given":"Runsheng","family":"Chen","sequence":"additional","affiliation":[{"name":"Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences 3 \u00a0 3 \u00a0 \u00a0 Beijing 100101, China"}]},{"given":"Xing Wang","family":"Deng","sequence":"additional","affiliation":[{"name":"Center of Bioinformatics & Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University 1 \u00a0 1 \u00a0 \u00a0 Beijing 100871, China"},{"name":"Department of Molecular, Cellular, and Developmental Biology, Yale University 2 \u00a0 2 \u00a0 \u00a0 New Haven, CT 06520, USA"}]},{"given":"Songgang","family":"Li","sequence":"additional","affiliation":[{"name":"Center of Bioinformatics & Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University 1 \u00a0 1 \u00a0 \u00a0 Beijing 100871, China"}]}],"member":"286","published-online":{"date-parts":[[2006,10,12]]},"reference":[{"key":"2023012409391898900_b1","volume-title":"Statistical Algorithms Description Document.","author":"Affymetrix","year":"2002"},{"key":"2023012409391898900_b2","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409391898900_b3","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023012409391898900_b4","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gng015","article-title":"Summaries of affymetrix GeneChip probe level data","volume":"31","author":"Irizarry","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012409391898900_b5","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/ng1704","article-title":"Genome-wide transcription analyses in rice using tiling microarrays","volume":"38","author":"Li","year":"2006","journal-title":"Nat. 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