lumi specifications


Unique identifier OMICS_00770
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.26.4
Stability Stable
Maintained Yes


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lumi articles

lumi citations

PMCID: 5814175

[…] mrna was subjected to microarray analysis by illumina chip array., background correction, variance stabilization and robust spline normalization of the expression data was performed using the lumi package from bioconductor [52]. the normalized data was further analyzed for differential gene expression between erufosine treated and untreated cells using the limma package in r [53]. […]

PMCID: 5603607

[…] scanner and the intensities of the images were extracted using genomestudio (2010.3) methylation module (1.8.5) software. a three-step-based normalization procedure was performed using the lumi35 package available for bioconductor36 in the r statistical environment37. this consisted of color bias adjustment, background level adjustment and quantile normalization across arrays35. […]

PMCID: 5399393

[…] with the illumina dataset gse42133 we employed the preprocessed data provided in geo database, log2 transformed and quantile normalized using illumina genomestudio® software (version 1.1.1) and ‘lumi’ package in r and bioconductor [41]. additional file 2 (figure s1) shows the distribution of the samples after preprocessing, median-centered values indicate that the data are normalized […]

PMCID: 4172902

[…] mouseref-8 24 k array at the burnham institute (la jolla, ca). results were extracted with illumina genomestudio v2011.1, background corrected and variance stabilized in r/bioconductor using the lumi package [81,82] and modeled in the limma package [83]. microarray data are available from nih geo accession gse48818., complementary dna (cdna) was prepared from rna using high capacity cdna […]

PMCID: 4057609

[…] 27,578 cpg sites across the human genome. the arrays were scanned using an illumina beadarray reader and subsequently processed using the illumina genomestudio v.1 software package. the bioconductor lumi package was used for downstream data processing and normalisation [18]. briefly, dna probe methylation data were quality checked and then colour balance adjusted, background corrected and scaled […]

lumi institution(s)
Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA

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