Aroma.affymetrix protocols

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Aroma.affymetrix specifications

Information


Unique identifier OMICS_00703
Name Aroma.affymetrix
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.12
Stability Stable
Source code URL http://callr.org/install#aroma.affymetrix
Maintained Yes

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Publication for Aroma.affymetrix

Aroma.affymetrix in pipelines

 (5)
2018
PMCID: 5766593
PMID: 29330417
DOI: 10.1038/s41598-017-17704-4

[…] are reported., genome-wide human snp arrays 6.0 (affymetrix) were performed according to the manufacturer’s protocol. raw probe values were extracted from cel files and processed with the r package aroma.affymetrix version 3.1.0. samples were compared to reference values, which was the average of 53 diploid bcp-all and t-all samples. to correct for bias introduced by differences in gc content […]

2014
PMCID: 4220069
PMID: 25270265
DOI: 10.1186/s13059-014-0470-7

[…] manuscript., we thank henrik bengtsson at university of california, san fransisco, usa and pierre neuvial, cnrs, france for useful discussions on baf bias, and henrik also for advice on using the aroma.affymetrix and pscbs r packages. we also like to acknowledge marcus mayrhofer at uppsala university, sweden for introducing us to two-dimensional patterns in snp array data in the form of taps […]

2014
PMCID: 4535873
PMID: 26484062
DOI: 10.1016/j.gdata.2014.02.004

[…] were thus carried out between homogenous samples., nexus copy number 6.0 (biodiscovery, inc., ca, usa) was used to assess genome wide copy number frequencies for the 15 patients. furthermore, aroma.affymetrix – another cbs implementation as part of the bioconductor's dnacopy library and the associated tumorboost algorithm (which normalize allele specific copy numbers for tumor samples […]

2013
PMCID: 3813709
PMID: 24204606
DOI: 10.1371/journal.pone.0076251

[…] were thus carried out between homogenous samples., nexus copy number 6.0 (biodiscovery, inc., ca, usa) was used to assess genome wide copy number frequencies for the 15 patients. further, aroma.affymetrix – another cbs implementation as part of bioconductor's dnacopy library and the associated tumorboost algorithm (which normalize allele specific copy numbers for tumor samples […]

2010
PMCID: 2937017
PMID: 20844748
DOI: 10.1371/journal.pone.0011408

[…] files for 163 samples were downloaded from the data portal (http://tcga-data.nci.nih.gov/tcga/homepage.htm)., all snp mapping arrays were first normalized using methods available in the r package “aroma.affymetrix” , including techniques to remove systematic biases introduced due to allelic cross talk, pcr fragment length bias and differences in gc content. dna copy number was estimated probe […]


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Aroma.affymetrix in publications

 (105)
PMCID: 5945577
PMID: 29467494
DOI: 10.1038/s41388-018-0129-z

[…] of this distance. a firma score of 1 indicates that no splicing has occurred. firma scores were compared using bayesian statistics. firma was performed using the default implementation of the aroma.affymetrix package in r together with logarithmic transformation, as described in the human exon array analysis vignette [, ]. a custom chip description file covering the exon array core […]

PMCID: 5810006
PMID: 29433456
DOI: 10.1186/s12885-018-4021-6

[…] were profiled using nugen amplification protocol and hybridized using the hrsta-2.0 custom human affymetrix array gpl10379. the microarray gene expression analyses were performed in r using the aroma.affymetrix package. the pam50 intrinsic subtypes (pam50) for cohort 1 relapses have been previously published [] and publicly available gse56493. the case-control cohort have been previously […]

PMCID: 5799174
PMID: 29402961
DOI: 10.1038/s41598-018-20161-2

[…] from cancer biomedical informatics grid (cabig) portal and all samples were profiled using affymetrix human genome u133 plus 2.0 array platform. the raw cel files data was normalized using the aroma affymetrix (version 1.3.0) r package (http://www.aroma-project.org) based on custom cdf files (version 16) found at http://brainarray.mbni.med.umich.edu.connectivity map (cmap) microarray […]

PMCID: 5772473
PMID: 29343721
DOI: 10.1038/s41467-017-02408-0

[…] the intensity data were subjected to quantile normalisation and summarisation using the rma algorithm in the r ‘affy’ and ‘aroma.affymetrix’ packages. analysis was then performed on transcript-level probesets using the core annotations. at the transcript level, 18 707 probesets represented different transcripts., […]

PMCID: 5766593
PMID: 29330417
DOI: 10.1038/s41598-017-17704-4

[…] are reported., genome-wide human snp arrays 6.0 (affymetrix) were performed according to the manufacturer’s protocol. raw probe values were extracted from cel files and processed with the r package aroma.affymetrix version 3.1.0. samples were compared to reference values, which was the average of 53 diploid bcp-all and t-all samples. to correct for bias introduced by differences in gc content […]


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Aroma.affymetrix institution(s)
Department of Statistics, University of California, Berkeley, CA, USA

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