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arrayQuality specifications


Unique identifier OMICS_02020
Name arrayQuality
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.58.0
Stability Stable
limma, methods, stats, RColorBrewer, grid, graphics, utils, grDevices, gridBase, mclust, marray, R(>=2.2.0), hexbin, MEEBOdata, HEEBOdata
Maintained Yes


No version available


arrayQuality citations


Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1 Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins

Front Microbiol
PMCID: 5859033
PMID: 29593668
DOI: 10.3389/fmicb.2018.00380

[…] was used to detect the gene expression., pheno-data files of this dataset were prepared in identifiable format and missing values imputed (troyanskaya et al., ). the bioconductor packages including arrayquality metrics on r version 3.1.3 were used to execute the preprocessing steps of normalization and quality control (bolstad et al., ; fujita et al., ; obenchain et al., ). robust multi-array […]


Identification of key lncRNAs in colorectal cancer progression based on associated protein–protein interaction analysis

PMCID: 5553992
PMID: 28797257
DOI: 10.1186/s12957-017-1211-7

[…] number gse64857. this dataset was acquired from the study by wang []. totally, 81 samples were included in this dataset, which consisted of 44 stage ii and 37 stage iii crc samples. we used arrayquality package to quality control and limma package to apply raw data in r software. the normalization criteria were quantile normalization. genes having fold changes ≥2 and p values <0.05 […]


Cellular Signaling Pathways in Insulin Resistance Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus

Front Physiol
PMCID: 5264126
PMID: 28179884
DOI: 10.3389/fphys.2017.00013

[…] we organized the pheno-data files of this dataset in recognizable format (troyanskaya et al., ). the data was normalized to the median expression level of each gene using the bioconductor “arrayquality metrics” package (bolstad et al., ; fujita et al., ; obenchain et al., ). the expression of a transcript with detection p-value 0.15 was considered marginal. we log transformed […]


Ovarian tumour growth is characterized by mevalonate pathway gene signature in an orthotopic, syngeneic model of epithelial ovarian cancer

PMCID: 5216946
PMID: 27329838
DOI: 10.18632/oncotarget.10121

[…] labelled using agilent's low rna input amplification kit for 2-colour design for hybridizing to the whole mouse genome array (agilent)., quality control of expression data was confirmed using the arrayquality package in r and bioconductor []. data was preprocessed and normalized using agilent's spatial detrending normalization and imported into genespring for analysis. data was log (base 2) […]


Interleukin 6 is a potential therapeutic target in interleukin 6 dependent, estrogen receptor α positive breast cancer

PMCID: 4745841
PMID: 26893580
DOI: 10.2147/BCTT.S92414

[…] data were normalized with robust multiarray analysis and summarized with the hg-u219h sentrezg 15.0.0 chip definition files. single outlier arrays were set aside upon quality assessment with arrayquality metrics. genes that showed little expression variation across the samples were filtered out based on informative/noninformative calls, omitting 4,442 of the initial 18,567 genes […]


Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes in cell cycle and immune pathways associated with recurrence and response

PMCID: 4479083
PMID: 26021444
DOI: 10.1186/s13058-015-0582-3

[…] updated using the source database [], and the ucsc genome browser database and software tools [] were used for clones without unigene annotations. the quality of the arrays was analyzed using the arrayquality package in bioconductor., amplified rna samples were hybridized to six different batches of printed cdna microarrays. arrays in each print batch were normalized, and data from different […]

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