affylmGUI statistics

info info

Citations per year


Popular tool citations

chevron_left Differential expression detection chevron_right

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?


affylmGUI specifications


Unique identifier OMICS_02016
Name affylmGUI
Alternative name AffylmGUIR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Keith Satterley <>

Publication for affylmGUI

affylmGUI citations


GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6 LIKE 4 in Arabidopsis

PMCID: 5818008
PMID: 29439132
DOI: 10.1242/dev.159707

[…] extracted from three biological replicates and labeled probes were used for hybridization on ath1 chips (affymetrix). microarray data were analyzed using r software and the gcrma implementation with affylmgui () of the bioconductor package as previously described (; ). microarray data have been deposited in gene expression omnibus ( under accession number […]


Identification of the principal transcriptional regulators for low fat and high fat meal responsive genes in small intestine

PMCID: 5654052
PMID: 29075307
DOI: 10.1186/s12986-017-0221-3

[…] approach []. to correct the effect of multiple testing, the false discovery rate, was estimated from p values derived from the moderated t-test statistics []. the analysis was performed using the affylmgui graphical user interface for the limma microarray package []. genes were considered to be significantly differentially expressed if p-values were <0.05. under these conditions, a minimal […]


Targeting DMPK with Antisense Oligonucleotide Improves Muscle Strength in Myotonic Dystrophy Type 1 Mice

PMCID: 5453865
PMID: 28624222
DOI: 10.1016/j.omtn.2017.05.007

[…] of replicates. to correct for the effect of multiple testing, the false discovery rate was estimated from p values derived from the moderated t test statistics. the analysis was performed using the affylmgui graphical user interface for the limma microarray package and go analysis using the go enrichment functionality in the partek genomics suite software. for affymetrix mouse gene 2.0 st […]


Inappropriate expression of the translation elongation factor 1A disrupts genome stability and metabolism

PMCID: 5201016
PMID: 27807005
DOI: 10.1242/jcs.192831

[…] following reverse transcription reactions, the cdna template was hybridised to an affymetrix yeast 2.0 genechip array. data was quality controlled and normalised using the bioconductor plugin affylmgui (). to reduce background noise, we used the robust multi-array average (rma) algorithm (). a cut-off point was established for genes that were designated to have a b-statistic greater […]


Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis

PMCID: 5084710
PMID: 27666746
DOI: 10.1016/j.devcel.2016.08.013

[…] (qiagen) according to the manufacturer's instructions. agronomics1 arrays (affymetrix) were hybridized with labeled cdna following the manufacturer's instructions. to detect degs, we used the affylmgui package ( to run limma (linear models for microarray data) () using a chip description format (cdf) file for the agronomics1 array and tair10 […]


Gene Expression Differences in Peripheral Blood of Parkinson’s Disease Patients with Distinct Progression Profiles

PMCID: 4913914
PMID: 27322389
DOI: 10.1371/journal.pone.0157852

[…] to the analysis (leaving 17,011 of the 20,014 interrogated genes for analysis). the first method for the evaluation of differential expression included an f test (using the bioconductor r package affylmgui, r version 2.13.1)[]. additionally, we removed covariate effects including hybridization batch, age and gender by a linear empirical bayes model [] (). the expression data was analysed […]

Want to access the full list of citations?
affylmGUI institution(s)
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

affylmGUI reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review affylmGUI