R/maanova statistics

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R/maanova specifications

Information


Unique identifier OMICS_07680
Name R/maanova
Alternative names MicroArray ANalysis Of VAriance, MAANOVA
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 No

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Publication for MicroArray ANalysis Of VAriance

R/maanova citations

 (98)
library_books

Brain region specific expression of genes mapped within quantitative trait loci for behavioral responsiveness to acute stress in Fisher 344 and Wistar Kyoto male rats

2018
PLoS One
PMCID: 5847310
PMID: 29529077
DOI: 10.1371/journal.pone.0194293

[…] s, and hierarchical clustering of samples, as previously described []. Statistical significance of microarray expression differences between F344 and WKY was determined using ANOVA methods within the R/maanova package as previously described [, ]. DEGs were determined between strains with an FDR-adjusted P–value less than 0.05 and a fold change greater than 1.3 (30% increase or decrease). This cri […]

library_books

Stat 6 signaling pathway and not Interleukin 1 mediates multi walled carbon nanotube induced lung fibrosis in mice: insights from an adverse outcome pathway framework

2017
PMCID: 5598059
PMID: 28903780
DOI: 10.1186/s12989-017-0218-0

[…] nd heat maps of the raw and normalized data. Differentially expressed genes (DEGs)—increasing or decreasing relative to the lung tissue samples from age matched control mice—were determined using the MicroArray ANalysis Of VAriance (MAANOVA) library in R. This statistical model included the fixed effects slide and treatment condition, and was applied to the log2 of the relative intensities. The Fs […]

call_split

Characterization of bovine embryos cultured under conditions appropriate for sustaining human naïve pluripotency

2017
PLoS One
PMCID: 5328396
PMID: 28241084
DOI: 10.1371/journal.pone.0172920
call_split See protocol

[…] y, Hawthorne, CA, USA), Loess normalization was performed [] on mean spot-intensities. Correction of gene specific dye bias was performed by a within set estimate [] and data were further analyzed by MAANOVA [], modelling sample, array and dye effects in a fixed effect analysis. By a permutation F2-test, in which residuals were shuffled 10,000 times globally, p-values were determined. After false […]

library_books

A framework for the use of single chemical transcriptomics data in predicting the hazards associated with complex mixtures of polycyclic aromatic hydrocarbons

2016
PMCID: 5489644
PMID: 27858113
DOI: 10.1007/s00204-016-1891-8

[…] ing the R (R Development Core Team ) platform. A transcript was considered to be a differentially expressed gene (DEG: upregulated or downregulated relative to the vehicle treated controls) using the MAANOVA library in R (Wu et al. ). The Fs statistic was used to test for treatment effects (Cui et al. ). The P values for all statistical tests for each probe ID were estimated by the permutation met […]

library_books

Toxicogenomics analysis of mouse lung responses following exposure to titanium dioxide nanomaterials reveal their disease potential at high doses

2016
PMCID: 5180171
PMID: 27760801
DOI: 10.1093/mutage/gew048

[…] e microarray data, normalised using LOcally WEighted Scatterplot Smoothing (LOWESS) regression modelling method and statistical significance of the differentially expressed genes was determined using MicroArray ANalysis Of VAriance (MAANOVA) in R statistical software (http://www.r-project.org). The Fs statistic () was used to test the treatment effects compared with the matched controls exposed to […]

call_split

Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism

2016
Nucleic Acids Res
PMCID: 5175338
PMID: 27431323
DOI: 10.1093/nar/gkw643
call_split See protocol

[…] the fifth percentile and missing values subsequently imputed by flooring them at the fifth percentile. Differentially expressed genes were detected by analyzing the pre-processed data with a two-way MicroArray ANalysis Of Variance (MAANOVA) model (,) whereby genotype, treatment and the interaction of the two were terms in the model. Contrasts (t-tests) between treated samples and their respective […]

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R/maanova institution(s)
The Jackson Laboratory, Bar Harbor, ME, USA

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