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ArrayTools specifications

Information


Unique identifier OMICS_02022
Name ArrayTools
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
Version 1.40.0
Stability Stable
Requirements
limma, methods, stats, graphics, Biobase, utils, grDevices, affy, genefilter, Biobase(>=2.5.5), affydata, affy(>=1.23.4), R(>=2.7.0), xtable, R2HTML, affyPLM, gcrma, simpleaffy, annaffy, hugene10sttranscriptcluster.db
Maintained Yes

Versioning


No version available

Documentation


ArrayTools citations

 (16)
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Differential processing of small RNAs during endoplasmic reticulum stress

2017
Sci Rep
PMCID: 5408347
PMID: 28452371
DOI: 10.1038/srep46080
call_split See protocol

[…] ity control was conducted using Expression Console® Software. Genes were filtered by intensity compared with the control channel, and P ≤ 0.05 of a paired Student’s t-test was considered significant (ArrayTools was used for differential gene expression). For interpreting genome-wide expression profiles Gene Set Enrichment Analysis (GSEA) was applied. Microarray data are available in the ArrayExpre […]

library_books

Characterization of Arginase Expression in Glioma Associated Microglia and Macrophages

2016
PLoS One
PMCID: 5147798
PMID: 27936099
DOI: 10.1371/journal.pone.0165118

[…] Raw intensity measurements of all probe sets were background corrected, normalized and converted into expression measurements using the Affymetrix’s Expression Console v1.1.1. The Bioconductor “ArrayTools” package was then used to identify the genes differentially expressed between the samples. The corresponding p-values were adjusted using the false discovery rate (FDR) method to control th […]

library_books

An 8 gene mRNA expression profile in circulating tumor cells predicts response to aromatase inhibitors in metastatic breast cancer patients

2016
BMC Cancer
PMCID: 4759736
PMID: 26892682
DOI: 10.1186/s12885-016-2155-y

[…] as reported in the literature [, ]. In all 45 eligible patients, a leave-one-out-cross validation (LOOCV) was conducted using the Support Vector Machines (SVM) method within Biometric Research Branc ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) after selecting the top 75 % most variable genes from the 93 genes described above. With this LOOCV method, a gene signature was generated tha […]

call_split

Cytokine and Antibody Based Diagnostic Algorithms for Sputum Culture Positive Pulmonary Tuberculosis

2015
PLoS One
PMCID: 4682626
PMID: 26674517
DOI: 10.1371/journal.pone.0144705
call_split See protocol

[…] Statistical analyses were conducted using ArrayTools statistical software. Significance analysis of microarrays (SAM) was used for class comparison and selection of target cytokines. ROC curve analysis was performed with SPSS20.0. […]

call_split

A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease

2015
Nat Chem Biol
PMCID: 4677459
PMID: 26502155
DOI: 10.1038/nchembio.1952
call_split See protocol

[…] were hybridised to 8 × 60K mouse or human microarray following the manufacturers’ instructions (Agilent). Microrarray slides were washed, scanned and analysed. Mouse organoid data were analysed using Arraytools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and the colon cancer cell line data using Genespring (Agilent). A similar analysis was performed on both datasets. Lowess intensity dependent […]

call_split

Gene Expression Profiles Associated with Pediatric Relapsed AML

2015
PLoS One
PMCID: 4388534
PMID: 25849371
DOI: 10.1371/journal.pone.0121730
call_split See protocol

[…] luster 3.0 [] and visualized using Gene-E (http://www.broadinstitute.org/cancer/software/GENE-E/). Class comparison tests and class prediction tests were performed using the Biometric Research Branch Arraytools 4.2.1. Pathway analysis was performed using Ingenuity Pathway Analysis 7.5 software (Ingenuity Systems, Redwood City, CA, USA) based on the Ingenuity Pathways Knowledge Base. For details on […]

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