ArrayAnalysis.org protocols

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chevron_left Differential expression detection Data visualization Batch effect correction Normalization Quality control Topology enrichment analysis Bioinformatics workflows chevron_right
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ArrayAnalysis.org specifications

Information


Unique identifier OMICS_00742
Name ArrayAnalysis.org
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

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Information


Unique identifier OMICS_00742
Name ArrayAnalysis.org
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 ArrayAnalysis.org

ArrayAnalysis.org in pipeline

2015
PMCID: 4542440
PMID: 25979075
DOI: 10.2337/db15-0133

[…] 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 (http://arrayanalysis.org) with bioconductor (www.bioconductor.org). differentially expressed genes (degs) were determined using the intensity-based moderated t-statistic (ibmt) test () with a false […]


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ArrayAnalysis.org in publications

 (19)
PMCID: 5857180
PMID: 29556568
DOI: 10.1016/j.bbrep.2018.01.001

[…] 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 (http://www.arrayanalysis.org) . normalizing statistical analysis, multiple-testing corrections on p-value and generating annotations using geo2r software (www.ncbi.nlm.nih.gov/geo/geo2r). were performed using […]

PMCID: 5244361
PMID: 28102354
DOI: 10.1038/srep40901

[…] (the netherlands), according to affymetrix protocols. four to six biological replicates were used for each group. quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (maastricht university, the netherlands). normalization was done via the robust multichip average (rma) algorithm. due to a range in hybridization dates between fasting […]

PMCID: 5173369
PMID: 27997581
DOI: 10.1371/journal.pone.0168875

[…] 500 ng total rna with transcriptor reverse transcriptase (roche), according to the manufacturer’s instructions., each dataset obtained from the databases was uploaded to arrayanalysis [] (http://www.arrayanalysis.org/) for array correlation and signal-array comparability analysis. highly correlated (pearson’s r≥0.8) array datasets were selected after array correlation analysis., since […]

PMCID: 5161687
PMID: 27556946
DOI: 10.1038/nature19329

[…] at the microarray department of the university of amsterdam, the netherlands according to affymetrix protocols. quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (maastricht university, the netherlands)., the same total rna extracts were used as extracted for mrna analysis (above). mirna expression levels were assessed using a mirna […]

PMCID: 5005393
PMID: 27517371
DOI: 10.1007/s10354-016-0488-4

[…] was hybridized to affymetrix mouse genome 430 2.0 oligonucleotide arrays (moe430v2) (affymetrix, santa clara, usa) []. this dataset was uploaded and published on arrayexpress (e-geod-8720) []., in arrayanalysis.org, namely the affyqc and statistics tool [], the quality of the selected raw transcriptomics data was controlled, the data were normalized using gc-rma, and statistically analyzed […]


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ArrayAnalysis.org 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

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