aroma.light protocols

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aroma.light specifications

Information


Unique identifier OMICS_01998
Name aroma.light
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.10.0
Stability Stable
Requirements
stats, R(>=2.15.2), R.methodsS3(>=1.7.1), R.oo(>=1.21.0), R.utils(>=2.6.0), matrixStats(>=0.52.2), princurve(>=1.1-12)
Maintained Yes

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aroma.light in pipeline

2016
PMCID: 5073650
PMID: 27843554
DOI: 10.1136/bmjdrc-2016-000273

[…] the background adjustment was performed by subtracting the median background values from the median expression values. data were processed using log2 and then normalized using the quantile function aroma.light package. the differentially expressed genes were identified using the f-test with benjamini-hochberg correction in order to compare between groups. these analyses were performed using […]


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aroma.light in publications

 (13)
PMCID: 5833437
PMID: 29415999
DOI: 10.1038/s41419-017-0241-y

[…] background values from the median expression values obtained by fe, and data were subsequently log-transformed. finally, all the data distribution was normalized by quantile function using the aroma-light bioconductor package. differentially expressed mirnas were identified using the t-test by multtest package. mirnas were considered to be of interest if p-values ≤ 0.01, fold-change ≥ 2.0 […]

PMCID: 5354780
PMID: 28039483
DOI: 10.18632/oncotarget.14253

[…] the median signals (gmediansignal and gbgmediansignal) were used. following background subtraction and log2 scale transformation, the normalization was performed using the quantile method with the aroma light package []. differentially expressed micrornas were obtained by rank product analysis using the rankprod package [], considering p-values and positive false predictions (pfp) ≤ 0.05. […]

PMCID: 5073650
PMID: 27843554
DOI: 10.1136/bmjdrc-2016-000273

[…] the background adjustment was performed by subtracting the median background values from the median expression values. data were processed using log2 and then normalized using the quantile function aroma.light package. the differentially expressed genes were identified using the f-test with benjamini-hochberg correction in order to compare between groups. these analyses were performed using […]

PMCID: 5047645
PMID: 27695061
DOI: 10.1371/journal.pone.0163855

[…] microarray quantification software (imaging research inc., ge healthcare, buckinghamshire, uk). normalization of data was performed by quantile in the r environment (version 2.11.0) using the aroma light package (http://www.bioconductor.org). statistical data were analyzed using the multiexperiment viewer (mev) software (version 3.1 available online at http://www.tm4.org/mev.html). […]

PMCID: 4955732
PMID: 27376469
DOI: 10.1038/ni.3494

[…] program (v 0.6.0) using the “union” option. after removing absent features (zero counts in all samples), the raw counts were converted to rpkm value followed by quantile normalization via r library ‘aroma.light’. then the quantile normalized rpkm values were filtered by setting a cutoff value of 1 and analyzed with the multiplot module in genepattern suite […]


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