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Protocols

affylmGUI specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Keith Satterley

Publication for affylmGUI

affylmGUI citations

 (72)
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GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6 LIKE 4 in Arabidopsis

2018
PMCID: 5818008
PMID: 29439132
DOI: 10.1242/dev.159707
call_split See protocol

[…] 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 (https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE1039 […]

call_split

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

2017
PMCID: 5654052
PMID: 29075307
DOI: 10.1186/s12986-017-0221-3
call_split See protocol

[…] ing 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 mea […]

call_split

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

2017
Mol Ther Nucleic Acids
PMCID: 5453865
PMID: 28624222
DOI: 10.1016/j.omtn.2017.05.007
call_split See protocol

[…] r 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 arrays […]

library_books

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

2016
PMCID: 5201016
PMID: 27807005
DOI: 10.1242/jcs.192831

[…] ctions. 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 than 1 […]

library_books

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

2016
Dev Cell
PMCID: 5084710
PMID: 27666746
DOI: 10.1016/j.devcel.2016.08.013

[…] columns (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 (http://bioinf.wehi.edu.au/affylmGUI/about.html) to run LIMMA (Linear Models for MicroArray data) () using a chip description format (CDF) file for the AGRONOMICS1 array and TAIR10 ( […]

library_books

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

2016
PLoS One
PMCID: 4913914
PMID: 27322389
DOI: 10.1371/journal.pone.0157852

[…] ior 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 for d […]


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

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