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Protocols specifications


Unique identifier OMICS_00742
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Affymetrix
Operating system Unix/Linux
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Unique identifier OMICS_00742
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Affymetrix
Programming languages PHP, R
Computer skills Basic
Stability Stable
Maintained Yes

Publications for citations


Gastric cancer biomarkers; A systems biology approach

PMCID: 5857180
PMID: 29556568
DOI: 10.1016/j.bbrep.2018.01.001

[…] th cancer and non-cancer samples. Expression data of the series GSE19826 were applied for annotating the network, performing quality control and pre-processing using ArrayAnalysis modules ( . Normalizing statistical analysis, multiple-testing corrections on p-value and generating annotations using GEO2R software ( Were performed using im […]


ALS disrupts spinal motor neuron maturation and aging pathways within gene co expression networks

Nat Neurosci
PMCID: 5003654
PMID: 27428653
DOI: 10.1038/nn.4345

[…] luded. These 17 in vivo laser-captured MN specimens came from individuals with an age range from 40 to 80 years (median age, 63 years).All CEL files considered for use in this study were submitted to to inspect RNA and microarray hybridization quality, and samples that failed to meet the recommended standards were removed from further analysis. Affymetrix GeneChip Human Genome U1 […]


Gene expression profile comparison in the penile tissue of diabetes and cavernous nerve injury induced erectile dysfunction rat model

PMCID: 4949699
PMID: 27437539
DOI: 10.4111/icu.2016.57.4.286

[…] vel of the crura. We expect that this diabetes-induced ED model will be a good comparison with our CNI-induced ED model. The quality of microarray data was assessed through the pipeline at for intensive and strict quality control test to filter out low-quality microarray samples []. We used the same criteria for high-quality samples described by Lee et al. []. All raw […]


Transcriptome signature for dampened Th2 dominance in acellular pertussis vaccine induced CD4+ T cell responses through TLR4 ligation

Sci Rep
PMCID: 4846868
PMID: 27118638
DOI: 10.1038/srep25064

[…] Quality control and normalization of Affymetrix CEL files were performed using the ArrayAnalysis website (, using the Robust Multichip Average (RMA) method and the MBNI custom CDF version 15. Normalized data consisted of Log2 transformed signal values for 17306 genes. All slides passed q […]


The Metabolic Syndrome and Microvascular Complications in a Murine Model of Type 2 Diabetes

PMCID: 4542440
PMID: 25979075
DOI: 10.2337/db15-0133
call_split See protocol

[…] ). Briefly, microarray files were Robust Multi-array Average normalized using the BrainArray Custom Chip Definition File version 15 (). Quality was assessed using the affyAnalysisQC R package ( with Bioconductor ( Differentially expressed genes (DEGs) were determined using the intensity-based moderated T-statistic (IBMT) test () with a false discovery […]


OVCAR 3 Spheroid Derived Cells Display Distinct Metabolic Profiles

PLoS One
PMCID: 4331360
PMID: 25688563
DOI: 10.1371/journal.pone.0118262

[…] L files corresponding to 3 replicated cultures of OCSC and OCC (GeneChip Human Genome U133 Plus 2.0 Array), generated as previously described [], were processed and normalized by GCRMA method ( and used for GSEA ( without pre-filtering of probe sets using the following parameters: OCC vs. OCSC as categorical phenotypes; signal-t […]


Looking to check out a full list of citations? institution(s)
Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, Netherlands; Department of Experimental Cardiology, Heart Failure Research Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands; Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands; Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen, Netherlands reviews

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