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LMGene specifications

Information


Unique identifier OMICS_02009
Name LMGene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.36.0
Stability Stable
Requirements
R(>=2.10.0), affy, survival, multtest, Biobase(>=2.5.5), affydata
Maintained Yes

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LMGene citations

 (12)
library_books

Heterogeneity of Synovial Molecular Patterns in Patients with Arthritis

2015
PLoS One
PMCID: 4415786
PMID: 25927832
DOI: 10.1371/journal.pone.0122104

[…] transformation described in [] was carried out in order to stabilize the variance on the whole range of signal intensity. its parameters were tuned by maximizing likelihood, using the r package lmgene. in a third step, a scale normalization based on internal standards and house-keeping genes was applied. in particular, for each replicate zijk, with k = 1, 2, 3, corresponding to patient […]

library_books

Genomic characterization of a three dimensional skin model following exposure to ionizing radiation

2012
PMCID: 3483859
PMID: 22915785
DOI: 10.1093/jrr/rrs063

[…] samples were filtered out, resulting in a final set of 15 964 probes.transformation and normalization of the data was performed to stabilize the variance and to eliminate systematic array bias. the lmgene 2.0 r package was used to estimate the parameters of the glog transformation, followed by quantile analysis [–]., the microarray data were processed by beadstudio 3.4.0 using […]

library_books

Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks

2012
BMC Genomics
PMCID: 3443446
PMID: 22594378
DOI: 10.1186/1471-2164-13-190

[…] appropriate data transformation is required. to satisfy the constant variance assumption, we transformed the probe intensities data (y) with the transes function from bioconductor package lmgene. this package was developed from our lab and is designed for analysis of gene expression microarray data (see lmgene package in r). it applies g-log transform (generalised log transformation) […]

library_books

Transcriptomic Analysis of Toxoplasma Development Reveals Many Novel Functions and Structures Specific to Sporozoites and Oocysts

2012
PLoS One
PMCID: 3278417
PMID: 22347997
DOI: 10.1371/journal.pone.0029998

[…] the bioconductor package affy (version 1.22.1, ) within the statistical software system r (version 2.10.1, ), and transformed via a generalized logarithm transformation , using bioconductor package lmgene (version 2.4.0, )., a one-way analysis of variance (anova) model was fitted to the data one probeset at a time. the anova model included a single factor for time/lifestage, with the following […]

library_books

Small Protein Mediated Quorum Sensing in a Gram Negative Bacterium

2011
PLoS One
PMCID: 3236232
PMID: 22174954
DOI: 10.1371/journal.pone.0029192

[…] the metadata associated with the hybridizations, along with the “raw” intensities obtained from the genepix quantitation., to identified differentially expressed genes from metadata, the lmgene package for r language statistic analysis that computes the p-values per gene via gene by gene anova method developed by rocke was used . genes that were differentially expressed […]

library_books

Impact of the spotted microarray preprocessing method on fold change compression and variance stability

2011
BMC Bioinformatics
PMCID: 3224096
PMID: 22026942
DOI: 10.1186/1471-2105-12-413

[…] by durbin et al. [] and huber et al. [] to stabilize the variance. the glog transformation and the estimation of α and λ parameters are implemented in the transes and the tranest functions of the lmgene bioconductor package []. to allow comparison with the log2 transformation, glog transformed intensities (which are in the natural log scale) were multiplied by log2(e). practically, the glog […]


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