arrayQuality protocols

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arrayQuality specifications

Information


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
Requirements
limma, methods, stats, RColorBrewer, grid, graphics, utils, grDevices, gridBase, mclust, marray, R(>=2.2.0), hexbin, MEEBOdata, HEEBOdata
Maintained Yes

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arrayQuality in pipelines

 (2)
2015
PMCID: 4406155
PMID: 25512250
DOI: 10.1002/art.38995

[…] as previously described ()., quality control of microarray data was conducted using a harshlight package (http://asterion.rockefeller.edu/harshlight/index2.html) () and arrayquality control packages in r (http://www.r-project.org/). a gc-rma algorithm was used to calculate expression values (). expression values across diseases for skin and synovium were adjusted […]

2011
PMCID: 3195753
PMID: 21952044
DOI: 10.1186/1746-4811-7-29

[…] in both channels, as well as visually bad or contaminated spots, were flagged out. further data analysis was performed with r/bioconductor packages. hybridization quality was assessed with arrayquality [] and arrayqualitymetrix []. limma was used for normalization and assessing gene differential expression []. data filtering and other calculations were made in microsoft office excel […]


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arrayQuality in publications

 (20)
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 […]

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 […]

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 […]

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) […]

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 […]


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