ArrayPipe protocols

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chevron_left Background correction Gene expression microarray data visualization Bioinformatics workflows Differential expression detection Normalization Data preprocessing chevron_right
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ArrayPipe specifications

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Unique identifier OMICS_00744
Name ArrayPipe
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for ArrayPipe

ArrayPipe in pipelines

 (4)
2016
PMCID: 4959778
PMID: 27454487
DOI: 10.1371/journal.ppat.1005772

[…] rnas. arrays were scanned at 5 μm resolution using a genepix4000b scanner (molecular devices). data from scanned images were extracted using genepix 6.1 (axon) and processed and normalized using arraypipe (v2.0). processed data was used as input for linear modeling using bioconductor's limma package, which estimates the fold-change between predefined groups by fitting a linear model […]

2012
PMCID: 3350556
PMID: 22438580
DOI: 10.1091/mbc.E11-06-0532

[…] (molecular devices, sunnyvale, ca). spots were found and quantitated with genepix pro (molecular devices). data were analyzed as previously described (). hybridization data were preprocessed using arraypipe 1.7 (). background was subtracted using the “foreground–background” correction method, and the data were normalized using the limma loess (subgrid) method. genome-wide location data […]

2010
PMCID: 2922086
PMID: 20663191
DOI: 10.1186/1475-2859-9-60

[…] to rrna., data extracted with imagene 5.6 (biodiscovery, el segundo, ca, usa) were treated with homemade scripts in python language http://www.python.org and a local installation of the arraypipe web server []. probes showing a signal smaller than twice the standard deviation of the local background were considered without signal. probes showing no signal or saturated signals […]

2007
PMCID: 1941753
PMID: 17696614
DOI: 10.1371/journal.pgen.0030134

[…] microarray images were processed with genepix pro 6.0 (molecular devices, http://www.moleculardevices.com). data were analysed as described previously []. hybridization data were preprocessed with arraypipe 1.7 [], the background was subtracted using the “foreground-background” correction method, the data were normalized using the “linear model for microarray analysis (limma) loess (subgrid) […]


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ArrayPipe in publications

 (18)
PMCID: 5744066
PMID: 29375548
DOI: 10.3389/fimmu.2017.01828

[…] raw data are inherently a relative ratio of gene expression in the cgd cells to that in the control cells (with expression in the control sample = 1) with statistical significance determined by arraypipe software (in-house) as previously described (). p-values equal to or less than 0.05 were regarded significant and are indicated by (*) p < 0.05, (**) p < 0.01, or (***) p < 0.001., […]

PMCID: 5469186
PMID: 28606090
DOI: 10.1186/s12951-017-0278-1

[…] extraction from images was done using feature extraction software version 10.7 (agilent, usa). we further obtained normalized fold change values for all genes present on the microarray slides using arraypipe (v2.0). differentially regulated genes at various conditions were functionally clustered using web-based geneset analysis toolkit (webgestalt)., all graphs and statistical analysis […]

PMCID: 5448750
PMID: 28558017
DOI: 10.1371/journal.pone.0177977

[…] than one group, we prioritised the groups as presented., we performed k-means clustering with the euclidean distance method on the developmental dataset using the clustering module integrated in arraypipe (http://www.pathogenomics.ca/arraypipe—version 1.7)[]. each clustering analysis was iterated a thousand times., we performed chi square statistics to determine whether our developmental […]

PMCID: 4959778
PMID: 27454487
DOI: 10.1371/journal.ppat.1005772

[…] rnas. arrays were scanned at 5 μm resolution using a genepix4000b scanner (molecular devices). data from scanned images were extracted using genepix 6.1 (axon) and processed and normalized using arraypipe (v2.0). processed data was used as input for linear modeling using bioconductor's limma package, which estimates the fold-change between predefined groups by fitting a linear model […]

PMCID: 4668568
PMID: 26631971
DOI: 10.1038/srep17653

[…] scanner (axon instruments). quantification of fluorescent spot intensities and local background data was performed using the genepix 3.0 software supplied. microarray data files were loaded into arraypipe for quality assessment and for normalisation with the loess function applied to each sub-grid. multiple probes per gene were merged into one average value using the median. […]


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ArrayPipe institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Inimex Pharmaceuticals Inc., Vancouver, BC, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada; VIDO, Saskatoon, SK, Canada

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