lumi protocols

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lumi specifications

Information


Unique identifier OMICS_00770
Name lumi
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 2.32.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, RColorBrewer, graphics, GenomicRanges, stats4, lattice, R(>=2.10), GenomicFeatures, preprocessCore, MASS, genefilter, Biobase(>=2.5.5), vsn, affy(>=1.23.4), methylumi(>=2.3.2), annotate, mgcv(>=1.4-0), nleqslv, KernSmooth, RSQLite, DBI, beadarray, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping
Maintained Yes

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Publications for lumi

lumi in pipelines

 (101)
2018
PMCID: 5786503
PMID: 29275859
DOI: 10.1016/j.cell.2017.11.042

[…] of the housekeeping gene (adapted from )., raw intensity values of gene expression were extracted from microarray data using illumina genomestudio software and quantile normalized using r package lumi. normalized expression values were then log2 transformed. hierarchical clustering of samples was performed using pearson correlation and the ward. d2 agglomeration method on log2-transformed […]

2018
PMCID: 5838215
PMID: 29507296
DOI: 10.1038/s41398-018-0102-1

[…] labeling and scanning. raw microarray scan files were exported using the illumina genomestudio software and loaded into r for downstream analysis using specific packages provided by bioconductor. lumi was used to detect outliers. r package (version 3.24.4.) was used to correct for technical batch effects, like rna extraction batch, rna extraction method, dnase treatment batch, crna labeling […]

2018
PMCID: 5844691
PMID: 29488879
DOI: 10.7554/eLife.30496.036

[…] used two-way anova with multiple tukey’s tests. differences were considered statistically significant at p-values<0.05., raw data were quantile normalized using the normalization method from the lumi package (). unsupervised clustering (uc) analysis of gene expression datasets was performed using the pvclust package of the r software (r)(). the robustness of the uc tree was tested […]

2018
PMCID: 5871764
PMID: 29593239
DOI: 10.1038/s41598-018-23703-w

[…] labeling and scanning. raw microarray scan files were exported using the illumina genomestudio software and loaded into r for downstream analysis using specific packages provided by bioconductor. lumi was used to detect outliers. combat from the sva r package was used to correct for technical batch effects, like rna extraction batch, rna extraction method, dnase treatment batch, crna […]

2018
PMCID: 5876118
PMID: 29287311
DOI: 10.1002/art.40408

[…] we retained 428,232 cpg sites in 229 samples (58 cd14+ monocyte samples, 57 cd19+ b cell samples, 56 cd4+ naive t cell samples, and 58 cd4+ memory t cell samples)., statistical analysis. using the lumi r package , , methylation β values were transformed to m values in order to better approximate the homoscedasticity assumption in most statistical analyses. for each ra clinical outcome, robust […]


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lumi in publications

 (305)
PMCID: 5885411
PMID: 29618387
DOI: 10.1186/s13048-018-0399-7

[…] gene expression changes., summary-level data from genomestudio (defaulted to have no normalization or background correction) were loaded into the r statistical environment (v3.0.2) using the lumi package (v2.12.0) from bioconductor []. the remaining samples were transformed using variance-stabilizing transformation (vst) and normalized using robust spline normalization. samples […]

PMCID: 5884535
PMID: 29617451
DOI: 10.1371/journal.pone.0194844

[…] average (rma) analysis from the bio-conductor r package oligo []. in the same way, illumina expression data (cohort 2) was pre-processed by applying quantile normalization (qn) from the r package lumi []. in both cases, genes with low variability expression values were discarded to reduce false-positive rates., data from both platforms were integrated with the virtualarray software r package […]

PMCID: 5945969
PMID: 29761124
DOI: 10.1002/acn3.560

[…] were run in triplicate. the sds version 2.3 software was used to analyze the raw data and to call the genotypes., microarray raw signal processing for the ucsf‐mac cohort was performed using the lumi package. first, within‐sample raw gene expression intensities were normalized using variance‐stabilized transformation (vst) and interarray normalization was performed with robust spline […]

PMCID: 5859395
PMID: 29554922
DOI: 10.1186/s12977-018-0409-2

[…] package edger [] and gene-level analysis was performed using mageck []. the ifnα induction data was generated using a dataset (gse46599) published by goujon et al. [] and re-analyzed using the lumi [] and limma [] bioconductor packages. when several probes were used for a single genes, fold induction values were averaged., viral stocks were quantified using an rt activity assay described […]

PMCID: 5841238
PMID: 29511161
DOI: 10.1038/s41426-017-0018-5

[…] of uniquely mapped reads ranged from 23 to 25 × 106 per sample., for array data analysis, first, raw expression data were background-corrected, log2-transformed and quantile-normalized using the lumi r package available through the bioconductor repository. probes with a “detection p-value” lower than 0.01 in at least one sample were selected. for the detection of differentially expressed […]


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

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