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PECA specifications

Information


Unique identifier OMICS_20068
Name PECA
Alternative name Probe-level Expression Change Averaging
Software type Application/Script
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 1.16.0
Stability Stable
Requirements
limma, affy, R(>=3.3), preprocessCore, aroma.affymetrix, genefilter, ROTS, aroma.core, SpikeIn
Maintained Yes

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Maintainers


  • person_outline Tomi Suomi <>
  • person_outline Tomi Suomi <>
  • person_outline Laura Elo <>

Publication for Probe-level Expression Change Averaging

PECA in publications

 (4)
PMCID: 5417831
PMID: 28302922
DOI: 10.1074/mcp.O117.067728

[…] absolute quantitation, label-free quantification, limit of quantification, monte carlo method, false discovery rate based on sequential monte carlo simulation, max planck institute of biochemistry, probe-level expression change averaging, protein quantification by peptide quality control, peptide spectrum match, retention time, stable isotope labeling by amino acids in cell culture, […]

PMCID: 3857324
PMID: 24349258
DOI: 10.1371/journal.pone.0082340

[…] data from each replicate. the quantile-normalized probe-level data was transformed into probe set-level signal log-ratios between each non-thp sample and the corresponding thp sample using the probe-level expression change averaging procedure , as described in geo (gse18017)., from the original preprocessed datasets, only those probe sets were retained that mapped to a unique entrez id. […]

PMCID: 2938108
PMID: 20467038
DOI: 10.1074/mcp.M900483-MCP200

[…] used the so-called random effect meta-analysis model to estimate representative expression ratios for each protein from the three biological replicates. the approach is conceptually similar to the probe-level expression change averaging procedure that we have successfully applied to combine data across gene expression microarray experiments (). for microarray applications, the method takes […]

PMCID: 2728531
PMID: 19607685
DOI: 10.1186/gb-2009-10-7-r77

[…] the model to:, (3) (equation 3), which allows the probeset-level expression change μ(uv)g = μug - μvg to be estimated directly using, for instance, the median over the probes. this type of probe-level expression change averaging approach peca has been shown to improve the detection of differential expression in gene expression microarray studies []. moreover, in case of replicated […]


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PECA institution(s)
Turku Centre for Biotechnology, Turku, Finland

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