Lumi
Encyclopedia
Lumi is the Finnish word for snow and comes from the Proto-Uralic
word lomi meaning snow http://fi.wiktionary.org/wiki/lumi. Different companies have used the word in their brand name. One of them is the Dutch company LUMI communication & training http://www.lumi.nu/. It was founded in 2007 by Marlou Gulikers.
lumi is also a free
, open source
and open development software project for the analysis and comprehension of Illumina
expression and methylation microarray data. The project was started in the summer of 2006 and set out to provide algorithms and data management tools of Illumina in the framework of Bioconductor
. It is based on the statistical
R programming language.
), updated probe-to-gene mapping and annotation using the latest release of RefSeq (nuIDblast), probe-intensity transformation (VST) and normalization (RSN), quality control (QA/QC) and preprocessing methods specific for Illumina methylation data. By extending the ExprSet object with Illumina-specific features, lumi is designed to work with other Bioconductor packages, such as Limma and GOstats to detect differential genes and conduct Gene Ontology analysis.
. Originally lumi was designed for the analysis of Illumina Expression BeadArray data. Starting from 2010 (version > 2.0), functions of analyzing Illumina methylation microarray data was added. The project team consists of Drs. Pan Du, Simon M. Lin, and Warren A. Kibbe. The project was started upon a request for collaboration from Dr. Serdar E. Bulun to analyze a set of new Illumina microarray data acquired at his lab on the study of the effect of retinoic acids on cancers. Dr. Pan Du led the software development of the project. lumi was the first software package to utilize the unique design of redundancy of beadArrays for the data transformation and normalization processes. The first release of lumi was on January 3, 2007 through the Bioconductor
website. Before its formal release, it was beta-tested at Norwegian Radiumhospital, Leiden University Medical Center, Universiteit van Amsterdam, Università degli Studi di Brescia, UC Davis, Wayne State University, NIH, M.D. Anderson Cancer Center, Case Western Reserve University, Harvard University, Washington University, and Walter and Eliza Hall Institute of Medical Research.
Proto-Uralic language
Proto-Uralic is the hypothetical language ancestral to the Uralic language family. The language was originally spoken in a small area in about 7000-2000 BC , and expanded to give differentiated protolanguages. The exact location of the area or Urheimat is not known, but the vicinity of the Ural...
word lomi meaning snow http://fi.wiktionary.org/wiki/lumi. Different companies have used the word in their brand name. One of them is the Dutch company LUMI communication & training http://www.lumi.nu/. It was founded in 2007 by Marlou Gulikers.
lumi is also a free
Free software
Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...
, open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
and open development software project for the analysis and comprehension of Illumina
Illumina (company)
Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
expression and methylation microarray data. The project was started in the summer of 2006 and set out to provide algorithms and data management tools of Illumina in the framework of Bioconductor
Bioconductor
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology....
. It is based on the statistical
Statistics
Statistics is the study of the collection, organization, analysis, and interpretation of data. It deals with all aspects of this, including the planning of data collection in terms of the design of surveys and experiments....
R programming language.
Features
The lumi package provides an analysis pipeline for probe-level Illumina expression and methylation microarray data, including probe-identifier management (nuIDNuID
The nucleotide universal IDentifier is designed to uniquely and globally identify oligonucleotide microarray probes. Oligonucleotide probes of microarrays that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's...
), updated probe-to-gene mapping and annotation using the latest release of RefSeq (nuIDblast), probe-intensity transformation (VST) and normalization (RSN), quality control (QA/QC) and preprocessing methods specific for Illumina methylation data. By extending the ExprSet object with Illumina-specific features, lumi is designed to work with other Bioconductor packages, such as Limma and GOstats to detect differential genes and conduct Gene Ontology analysis.
History
The lumi project was started in the summer of 2006 at the Bioinformatics Core Facility of the Robert H. Lurie Comprehensive Cancer Center, Northwestern UniversityNorthwestern University
Northwestern University is a private research university in Evanston and Chicago, Illinois, USA. Northwestern has eleven undergraduate, graduate, and professional schools offering 124 undergraduate degrees and 145 graduate and professional degrees....
. Originally lumi was designed for the analysis of Illumina Expression BeadArray data. Starting from 2010 (version > 2.0), functions of analyzing Illumina methylation microarray data was added. The project team consists of Drs. Pan Du, Simon M. Lin, and Warren A. Kibbe. The project was started upon a request for collaboration from Dr. Serdar E. Bulun to analyze a set of new Illumina microarray data acquired at his lab on the study of the effect of retinoic acids on cancers. Dr. Pan Du led the software development of the project. lumi was the first software package to utilize the unique design of redundancy of beadArrays for the data transformation and normalization processes. The first release of lumi was on January 3, 2007 through the Bioconductor
Bioconductor
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology....
website. Before its formal release, it was beta-tested at Norwegian Radiumhospital, Leiden University Medical Center, Universiteit van Amsterdam, Università degli Studi di Brescia, UC Davis, Wayne State University, NIH, M.D. Anderson Cancer Center, Case Western Reserve University, Harvard University, Washington University, and Walter and Eliza Hall Institute of Medical Research.
See also
- BioconductorBioconductorBioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology....
, integrated software for the statistical analysis of wet lab data in molecular biology
- Illumina Inc.Illumina (company)Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
and its beadArray technology