IMA protocols

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chevron_left Differentially methylated region detection Differential methylation site detection Background correction chevron_right
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Associated diseases

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IMA specifications

Information


Unique identifier OMICS_00795
Name IMA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for IMA

IMA in pipelines

 (2)
2014
PMCID: 4165320
PMID: 25278959
DOI: 10.3389/fgene.2014.00324

[…] array has been dedicated to normalization and filtering (e.g., price et al., ; aryee et al., ) and various options for inferring dm sites from 27k/450k array data have been proposed. to test for dm, ima proposes wilcoxon rank-sum tests on beta-values (wang et al., ). cohcap operates either on methylation array data or bs-seq data, using beta-values or methylation proportions as input; they offer […]

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

[…] have been shrunk towards a common value. m-values should be used in these cases as, being based on a bayesian gaussian model, they will rely much more heavily on the gaussianity assumption (). the ima package () allows site (methylation locus)-specific and region (all loci in a gene)-specific differential methylation analysis using student's t-test and empirical bayes statistics. for region […]


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IMA in publications

 (17)
PMCID: 5928889
PMID: 29721079
DOI: 10.7150/thno.23544

[…] et al. was used to map the reads from the ion torrent pgm to the reference genome ., all analyses were performed using the statistical software environment r including packages survival, champ, ima, rocr as well as brb array tools for class prediction, and genesis for hierarchical clustering and heatmap visualization., after quantile normalization and type i/ii peak correction, […]

PMCID: 5482123
PMID: 28498449
DOI: 10.3892/mmr.2017.6581

[…] constructed. for gse40870, the differentially methylated sites were identified in aml cells treated with decitabine compared with cytarabine via the illumina methylation analyzer () package of r (ima.r-forge.r-project.org/), and were screened out with the criteria p<0.05 and log(fold-change)>0.2., gene ontology (go) enrichment analysis of degs was performed via the database […]

PMCID: 5367832
PMID: 28346544
DOI: 10.1371/journal.pone.0174699

[…] to standardize data, following the δcq method., microarray intensities were intra-array and inter-array normalized using limma software [] for mrna data, agimicrorna software [] for mirna data, and ima software [] for methylation data. these tools are available as bioconductor packages in the r statistical computing environment. the methylation level for each gene was calculated as the mean […]

PMCID: 4907103
PMID: 27347167
DOI: 10.3892/ol.2016.4658

[…] [cpg sites (p>0.05)/all cpg sites >1/100,000] were first excluded. peak standardization was then performed for the remaining cpg sites and samples using the illumina methylation analyzer (ima) package ()., the normalized data gse55940 were further analyzed by limma package (), and genes with p<0.05 and |log[fold change (fc)]|>0.5 were defined as degs., for the data gse46306, […]

PMCID: 4786116
PMID: 26963385
DOI: 10.1371/journal.pone.0150629

[…] signal ranging from 0 to 1, representing completely unmethylated to completely methylated values, respectively. methylation data was preprocessed in r using the illumina methylation analyzer (ima) package []. data preprocessing included background correction, probe scaling to balance infinium i and ii probes, quantile normalization, and logit transformation. a logit transformation […]


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IMA institution(s)
Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, USA

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