lumi: a pipeline for processing Illumina microarray
By Pan Du, Warren A. Kibbe, Simon M. Lin. Bioinform., 2008
2,187 citations recorded by the source corpus.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c1470d1b6302f7a5bb0911ac40179d940e10b232
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In Genetics
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- Peter Donnelly
- Z. Su
- Stephen Leslie
- Bruno Iochins Grisci
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In Molecular Biology
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Citations in the corpus
- Batch effect removal methods for microarray gene expression data integration: a survey (2013, methodology): “…that the gene expression data have been log-transformed and preprocessed (using either MAS5 [31], RMA [32], fRMA [33] for Affymetrix platforms or the preprocessing tools provided by ‘lumi’ Bioconductor package for Illumina platforms [34]) for background correction, normalization and summarization.”
- CuMiDa: An Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research (2019, methodology): “We employed the packages: (1) affy (Gautier et al., 2004) for Affymetrix data sets; (2) lumi (Du et al., 2008), beadarray (Dunning et al., 2007), and illuminaio (Smith et al., 2013) for Illumina microarrays; and (3) the package limma (Ritchie et al., 2015) for Agilent and other platforms, when…”
- A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue (2013, neutral): “…further analysis, the DNA methylation data was exported from GenomeStudio and subsequently analyzed using Bioconductor [56] and the lumi package [57]. b -values were converted to M-values (M = log 2 ( b /(1-b ))), a more statistically valid method for conducting differential methylation…”
- Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma (2017, methodology): “Gene expression microarray data was pre-processed using the “lumi” R package (69).”
- Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility (2011, methodology): “Data was processed in GenomeStudio (Illumina) and analyzed using Lum”