{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:43:19Z","timestamp":1771375399301,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2024,10,3]],"date-time":"2024-10-03T00:00:00Z","timestamp":1727913600000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["T32 CA233399"],"award-info":[{"award-number":["T32 CA233399"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","award":["IRG-21-145-25"],"award-info":[{"award-number":["IRG-21-145-25"]}],"id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Integrative analysis of heterogeneous expression data remains challenging due to variations in platform, RNA quality, sample processing, and other unknown technical effects. Selecting the approach for removing unwanted batch effects can be a time-consuming and tedious process, especially for more biologically focused investigators.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present BatchFLEX, a Shiny app that can facilitate visualization and correction of batch effects using several established methods. BatchFLEX can visualize the variance contribution of a factor before and after correction. As an example, we have analyzed ImmGen microarray data and enhanced its expression signals that distinguishes each immune cell type. Moreover, our analysis revealed the impact of the batch correction in altering the gene expression rank and single-sample GSEA pathway scores in immune cell types, highlighting the importance of real-time assessment of the batch correction for optimal downstream analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Our tool is available through Github https:\/\/github.com\/shawlab-moffitt\/BATCH-FLEX-ShinyApp with an online example on Shiny.io https:\/\/shawlab-moffitt.shinyapps.io\/batch_flex\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae587","type":"journal-article","created":{"date-parts":[[2024,10,3]],"date-time":"2024-10-03T14:17:32Z","timestamp":1727965052000},"source":"Crossref","is-referenced-by-count":1,"title":["BatchFLEX: feature-level equalization of X-batch"],"prefix":"10.1093","volume":"40","author":[{"given":"Joshua T","family":"Davis","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alyssa N","family":"Obermayer","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1251-9179","authenticated-orcid":false,"given":"Alex C","family":"Soupir","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0472-7517","authenticated-orcid":false,"given":"Rebecca S","family":"Hesterberg","sequence":"additional","affiliation":[{"name":"Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thac","family":"Duong","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ching-Yao","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ken Phong","family":"Dao","sequence":"additional","affiliation":[{"name":"Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brandon J","family":"Manley","sequence":"additional","affiliation":[{"name":"Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G Daniel","family":"Grass","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dorina","family":"Avram","sequence":"additional","affiliation":[{"name":"Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paulo C","family":"Rodriguez","sequence":"additional","affiliation":[{"name":"Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7739-7956","authenticated-orcid":false,"given":"Brooke L","family":"Fridley","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]},{"name":"Department of Malignant Hematology, Children\u2019s Mercy , Kansas City, MO 64108,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqing","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8536-8941","authenticated-orcid":false,"given":"Mingxiang","family":"Teng","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5775-408X","authenticated-orcid":false,"given":"Xuefeng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9316-1924","authenticated-orcid":false,"given":"Timothy I","family":"Shaw","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,10,3]]},"reference":[{"key":"2024101722010719400_btae587-B1","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1084\/jem.20110538","article-title":"CD103+ pulmonary dendritic cells preferentially acquire and present apoptotic cell-associated antigen","volume":"208","author":"Desch","year":"2011","journal-title":"J Exp Med"},{"key":"2024101722010719400_btae587-B2","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1158\/2326-6066.CIR-13-0209","article-title":"The tumor microenvironment shapes lineage, transcriptional, and functional diversity of infiltrating myeloid cells","volume":"2","author":"Elpek","year":"2014","journal-title":"Cancer Immunol 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Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae587\/59554859\/btae587.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/10\/btae587\/59835308\/btae587.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/10\/btae587\/59835308\/btae587.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T22:01:24Z","timestamp":1729202484000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae587\/7808854"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,10,1]]},"references-count":20,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2024,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae587","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,10]]},"published":{"date-parts":[[2024,10,1]]},"article-number":"btae587"}}