BMIQ protocols

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BMIQ specifications

Information


Unique identifier OMICS_02304
Name BMIQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for BMIQ

BMIQ in pipelines

 (8)
2018
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] we evaluated five methods using three real datasets, and proposed outperform methods for the illumina 450k array data analysis. minfi and methylumi are optimal choice when analyzing small dataset. bmiq and rcp are proper to correcting type bias and the normalized result of them can be used to discover dmps. r package missmethyl is suitable for go term enrichment analysis and biological […]

2017
PMCID: 5537648
PMID: 28654093
DOI: 10.1038/tp.2017.130

[…] data at the 485 557 cpg probes was performed as follows. probes with detection p-value >0.001 were set to missing, and probes with more than 20% missing were filtered. beta mixture quantile (bmiq) normalization was applied to the beta values for correction of bias due to the type i and type ii probes. non-specific, cross-hybridized probes,, probes overlapping with a single-nucleotide […]

2017
PMCID: 5559542
PMID: 28814741
DOI: 10.1038/s41598-017-08595-6

[…] mapping to sex chromosomes, associated with snps and/or out of cpg context were removed, and cpg probes and samples were filtered at detection p-value of 0.01. the beta mixture quantile dilation (bmiq) method was used for normalization., we studied a global methylation measure, genome-wide average dna methylation (gwam) defined as the average beta-value across autosomal probes. we compared […]

2016
PMCID: 5000688
PMID: 27517910
DOI: 10.3390/ijms17081291

[…] corrections and dye bias equalizations were performed using methylumi and lumi r packages, respectively [,]. signals were further normalized using the beta-mixture quantile normalization method (bmiq) []. briefly, cpgs with high quality (p < 0.05) were only used for analyses. each methylation data point was represented by fluorescent signals from the m (methylated) and u (unmethylated) […]

2016
PMCID: 5302953
PMID: 27462864
DOI: 10.18632/oncotarget.10792

[…] was performed by illumina genomestudio software, which were declared by the data contributor in geo database. and for gse54503 dataset, we also performed the beta-mixture quantile normalization (bmiq) []. furthermore, we downloaded dna methylation data with clinical data of hcc from the cancer genome atlas (tcga). data processing was performed using rnbeads software. we thus use […]


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BMIQ in publications

 (57)
PMCID: 5922319
PMID: 29695247
DOI: 10.1186/s12864-018-4652-7

[…] using out-of-band infinium1 intensities as well as correction for dye bias based on internal control probes []. data were then quantile normalized followed by beta mixture quantile dilation [bmiq] []. samples with insufficient dna quality (average of medians of methylated and unmethylated signals <10.5; outlier status with regard to either averaged total intensity values or beta value […]

PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] we evaluated five methods using three real datasets, and proposed outperform methods for the illumina 450k array data analysis. minfi and methylumi are optimal choice when analyzing small dataset. bmiq and rcp are proper to correcting type bias and the normalized result of them can be used to discover dmps. r package missmethyl is suitable for go term enrichment analysis and biological […]

PMCID: 5841757
PMID: 29513726
DOI: 10.1371/journal.pone.0193271

[…] p-values (p > .01) were considered to be unreliable and removed from analysis (n = 24,591), as recommended by the manufacturer. subsequently, data were normalized using the beta-mixture quantile (bmiq) normalization methodology []. this was performed using the watermelon package (version 1.11.0) in r (version 3.2.3; the r project for statistical computing) []. probes that represent known […]

PMCID: 5802688
PMID: 29249830
DOI: 10.1038/s41398-017-0026-1

[…] developed by horvath. this predictor was developed using 82 illumina dna methylation array datasets (n = 7,844) involving 51 healthy tissues and cell types. the raw data were normalized using bmiq normalization method implemented in the horvath dna methylation-based age predictor r script. we then tested whether epigenetic age acceleration (∆-age), calculated by subtracting the actual […]

PMCID: 5730612
PMID: 29242640
DOI: 10.1038/s41598-017-18034-1

[…] genosplice technology performed quality control, processing, and further analyses of the data. the data were normalised to adjust for assay type ii bias using the beta-mixture quantile dilation (bmiq) method from the chip analysis methylation pipeline (champ) r package. the 450 k array contains 65 single nucleotide polymorphism (snp) probes that do not interrogate methylation, […]


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BMIQ institution(s)
Statistical Genomics Group, UCL Cancer Institute, University College London, London, UK

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