Methylumi protocols

Methylumi specifications

Information


Unique identifier OMICS_00798
Name Methylumi
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 General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for Methylumi

Methylumi IN pipelines

 (4)
2016
PMCID: 5000688
PMID: 27517910
DOI: 10.3390/ijms17081291

[…] cpgs in the human genome. preprocessing of raw data was conducted using the genomestudio application by macrogen (macrogen). background corrections and dye bias equalizations were performed using methylumi and lumi r packages, respectively [37,38]. signals were further normalized using the beta-mixture quantile normalization method (bmiq) [39]. briefly, cpgs with high quality (p < 0.05) […]

2013
PMCID: 3572060
PMID: 23418593
DOI: 10.1371/journal.pone.0056702

[…] dna was extracted using dneasy blood & tissue kit (qiagen)., microarray data for gene expression and dna methylation were obtained from gse35913. the analyses were performed using r in lumi and methylumi environments [20]. heat map was generated using gplots package., tp53, cdkn2a and cdkn2b were amplified from cdna and genomic dna of imr90 (positive control), h358, h460 and 10 randomly […]

2013
PMCID: 3777004
PMID: 23982603
DOI: 10.1038/bjc.2013.496

[…] p-values, are available in r and bioconductor packages, such as the preprocessing and analysis pipeline (touleimat and tost, 2012), ima (wang et al, 2012), minfi (hansen and aryee, 2013) and methylumi (davis et al, 2011)., similar to sample quality control, it is customary to filter probes if a certain proportion of samples (i.e., >25%) have a detection p-value below a certain […]

2011
PMCID: 3568942
PMID: 22071477
DOI: 10.1038/jid.2011.348

[…] image processing, intensity data extraction and analyses were conducted with the beadarray reader., non-normalized methylation data were analyzed with the r (v2.12.0) bioconductor (biobase v2.10.0) methylumi (v1.4.0) and lumi (v2.2.0) packages (davis et al., 2010; du et al., 2008; gentleman et al., 2004; r development core team, 2010). supplementary figure 1 provides a description […]

Methylumi institution(s)
Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA, USA

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