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Protocols

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

Versioning


No version available

Documentation


Publication for Aroma.affymetrix

Aroma.affymetrix citations

 (81)
call_split

Alternative transcription of a shorter, non anti angiogenic thrombospondin 2 variant in cancer associated blood vessels

2018
Oncogene
PMCID: 5945577
PMID: 29467494
DOI: 10.1038/s41388-018-0129-z
call_split See protocol

[…] measure 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 probese […]

library_books

ITGB1 dependent upregulation of Caveolin 1 switches TGFβ signalling from tumour suppressive to oncogenic in prostate cancer

2018
Sci Rep
PMCID: 5799174
PMID: 29402961
DOI: 10.1038/s41598-018-20161-2

[…] loaded 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 datase […]

call_split

∆133p53 isoform promotes tumour invasion and metastasis via interleukin 6 activation of JAK STAT and RhoA ROCK signalling

2018
Nat Commun
PMCID: 5772473
PMID: 29343721
DOI: 10.1038/s41467-017-02408-0
call_split See protocol

[…] vel_seven_software_products_only.jsp?productId=131414&categoryId=35623#1_1), 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.∆133TP53 m […]

library_books

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

2018
Nat Commun
PMCID: 5750210
PMID: 29296022
DOI: 10.1038/s41467-017-02424-0

[…] yping analyses were carried out at Eurofins Genomics (Ebersberg, Germany) using the Affymetrix Mouse Diversity Array. The SNP arrays were processed, quantile-normalized, and median-polished using the Aroma Affymetrix CRMAv2 algorithm together with 351 publically available Mouse Diversity Genotyping Array CEL files which were downloaded from the Center for Genome Dynamics at The Jackson Laboratory […]

library_books

Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast

2017
PMCID: 5711926
PMID: 29214215
DOI: 10.1038/s41523-017-0048-0

[…] rison of gene copy number profiles of MBCs with those of common-type TNBCs, SNP 6.0 array data were obtained from triple-negative IDC-NSTs and matched in a 2:1 ratio with MBCs and processed using the aroma.affymetrix and DNAcopy packages as described above. […]

library_books

Integrative analysis of genome wide gene copy number changes and gene expression in non small cell lung cancer

2017
PLoS One
PMCID: 5675410
PMID: 29112949
DOI: 10.1371/journal.pone.0187246

[…] data of this study, in total 190 cases, has been deposited under accession number GSE76730. Copy numbers (CN) were estimated using Robust Multichip Analysis (CRMA v2) as implemented in the R package ‘aroma.affymetrix’ []. The preprocessing included quantile normalization [], fitting a log-additive probe-level model [] for probe summarization, combining the alleles and merging the strands, and frag […]


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

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