limmaGUI protocols

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limmaGUI specifications

Information


Unique identifier OMICS_02027
Name limmaGUI
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 1.56.1
Stability Stable
Requirements
limma, methods, graphics, utils, grDevices, xtable, R2HTML, tcltk, tkrplot
Maintained Yes

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Publication for limmaGUI

limmaGUI in pipelines

 (3)
2017
PMCID: 5549176
PMID: 28808688
DOI: 10.1128/mSphere.00167-17

[…] rrays were scanned on an agilent g2505c microarray scanner, and microarray scan data were extracted with agilent feature extraction software., raw gene expression microarray data were normalized with limmagui software (r/bioconductor, boston, ma) (). differentially expressed genes (degs) were extracted with limma () by using a differential threshold of 1.5 and a false discovery rate-corrected p va […]

2013
PMCID: 3733161
PMID: 23828547
DOI: 10.1093/jxb/ert185

[…] rosettes of four pooled plants, and the comparison of col-0 versus hsfa2ox was carried out using the catma (version 3) microarray (). normalization and analysis of the array was carried out using limmagui, a graphical front end for the limma (linear models for microarray; ) package for r available from bioconductor (http://www.bioconductor.org)., the publicly available microarray data sets […]

2010
PMCID: 2877315
PMID: 20372966
DOI: 10.1007/s00018-010-0341-7

[…] reference samples (cy3)., quality control for every microarray was performed visually by using ‘quality’ control graphs from ‘feature’ extraction and m-a plots and boxplots, which were made using limmagui in r (bioconductor) []. data were imported into genemaths xt 2.0 (applied maths, sint-martens-latem, belgium). spots with a cy5 and cy3 signal twice above background were selected […]

limmaGUI in publications

 (25)
PMCID: 5549176
PMID: 28808688
DOI: 10.1128/mSphere.00167-17

[…] rrays were scanned on an agilent g2505c microarray scanner, and microarray scan data were extracted with agilent feature extraction software., raw gene expression microarray data were normalized with limmagui software (r/bioconductor, boston, ma) (). differentially expressed genes (degs) were extracted with limma () by using a differential threshold of 1.5 and a false discovery rate-corrected p va […]

PMCID: 5475338
PMID: 28674541
DOI: 10.3389/fpls.2017.01006

[…] the probe values into probe set values, resulting in 22,811 normalized expression values per array. the r/bioconductor (gentleman et al., ) package limma (smyth, ) with the graphical user interface limmagui (wettenhall and smyth, ) was employed to pre-process the raw microarray data. analysis of variance (anova) in combination with the false discovery rate (fdr) test method were applied […]

PMCID: 5468566
PMID: 28659918
DOI: 10.3389/fimmu.2017.00679

[…] (affymetrix genechip mouse gene 1.0 st) and image scanning were performed according to the affymetrix expression analysis technical manual. gene expression microarray raw data were normalized using limmagui software (r/bioconductor, boston, ma, usa). data can be accessed through the geo repository accession number gse90831. microarrays data were analyzed with the ingenuity pathway analysis […]

PMCID: 5437943
PMID: 28327945
DOI: 10.1093/gigascience/gix015

[…] the utility of the associated with command-line interfaces but typically do not scale to large data sets. examples of genomics tools offering web-accessible guis include blast [], vague [], and limmagui []. however, beyond an inability to scale, web-based utilities pose several issues, including design inconsistency, redundant efforts in interface development, and the inability […]

PMCID: 4402510
PMID: 25605792
DOI: 10.1093/nar/gkv007

[…] limma package is used as a building block or as the underlying computational engine by a number of software projects designed to provide user-interfaces for gene expression data analysis including limmagui (), affylmgui (), webarray (), race (), carmaweb (), goulphar (), magma (), asterias (), genepattern (), geo2r (http://www.ncbi.nlm.nih.gov/geo/geo2r), the ebi expression atlas (), guide () […]

limmaGUI institution(s)
Division of Genetics and Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

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