RPA statistics

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RPA specifications

Information


Unique identifier OMICS_00778
Name RPA
Alternative name Robust Probabilistic Averaging
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.37.2
Stability Stable
Requirements
methods, parallel, BiocGenerics, affy, knitr, affydata, R(>=3.1.1), phyloseq
Maintained Yes

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Publications for Robust Probabilistic Averaging

RPA in publications

 (6)
PMCID: 5595324
PMID: 28898292
DOI: 10.1371/journal.pone.0184274

[…] and analyzed using a set of r-based scripts in combination with a custom-designed relational database, which operates under the mysql database management system. for microbial profiling, the robust probabilistic averaging (rpa) signal intensities of 2667 specific probes for the 94 genus-level bacterial groups detected on the mitchip, were used []. diversity calculations were performed […]

PMCID: 5054004
PMID: 27774093
DOI: 10.3389/fimmu.2016.00408

[…] and analyzed using a set of r-based scripts in combination with a custom-designed relational database, which operates under the mysql database management system. for the microbial profiling, the robust probabilistic averaging signal intensities of 2667 specific probes for the 94 genus-level bacterial groups detected on the mitchip were used (). diversity calculations were performed using […]

PMCID: 5515273
PMID: 28721246
DOI: 10.1038/npjbiofilms.2016.9

[…] and analysed using a set of r-based scripts in combination with a custom-designed relational database, which operates under the mysql database management system. for the microbial profiling, the robust probabilistic averaging signal intensities of 2667 specific probes for the 94 genus-level bacterial groups detected on the mitchip were used. diversity calculations were performed using […]

PMCID: 4600214
PMID: 26457177
DOI: 10.1186/s13395-015-0059-1

[…] records were not resolvable, and instead a group average and dispersion measure was given, t2d type 2 diabetes, data normalization was done on the raw .cel files for hg-u133a and hg-u133 + 2 using robust probabilistic averaging (rpa) [, ]. custom array definition files were created using the customcdf r/bioconductor package (v16), removing probes mapping to known snps, and summarizing probes […]

PMCID: 4557834
PMID: 26332837
DOI: 10.1371/journal.pone.0137347

[…] pearson correlation coefficient of the natural logarithm of spatially normalized signals, excluding outlier spots [], was considered indicative of satisfactory hitchip hybridization reproducibility. robust probabilistic averaging (rpa) was used to calculate relative abundance. the accuracy of each probe was determined and the less accurate probes were weighted lower in the summarization []. […]


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RPA institution(s)
Department of Veterinary Bioscience, University of Helsinki, University of Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Material Science and Engineering, Universidad Carlos III de Madrid, Leganés, Spain; Department of Mathematics and Statistics, University of Turku, Turku, Finland; Turku Centre for Biotechnology, Turku, Finland
RPA funding source(s)
This work was supported by Academy of Finland (256950, 127575, 218591), Alfred Kordelin foundation, Ramón Areces Foundation, European Community’s Seventh Framework Programme (FP7/2007-2013), ENGAGE Consortium (HEALTH-F4-2007-201413).

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