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affyPLM specifications

Information


Unique identifier OMICS_02017
Name affyPLM
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 1.56.0
Stability Stable
Requirements
methods, stats, graphics, grDevices, zlibbioc, MASS, R(>=2.6.0), affydata, Biobase(>=2.17.8), gcrma, BiocGenerics(>=0.3.2), affy(>=1.11.0), preprocessCore(>=1.5.1)
Maintained Yes

Versioning


No version available

Documentation


affyPLM citations

 (209)
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Pure flavonoid epicatechin and whole genome gene expression profiles in circulating immune cells in adults with elevated blood pressure: A randomised double blind, placebo controlled, crossover trial

2018
PLoS One
PMCID: 5908087
PMID: 29672527
DOI: 10.1371/journal.pone.0194229
call_split See protocol

[…] scribed in detail previously []. Briefly, normalized expression estimates of probe sets were computed by the robust multiarray analysis (RMA) algorithm [, ] as implemented in the Bioconductor library AffyPLM. Probe sets were redefined using current genome information according to Dai et al. [] based on annotations provided by the Entrez Gene database, which resulted in the profiling of 19,654 uniq […]

call_split

Species specific host factors rather than virus intrinsic virulence determine primate lentiviral pathogenicity

2018
Nat Commun
PMCID: 5893559
PMID: 29636452
DOI: 10.1038/s41467-018-03762-3
call_split See protocol

[…] Transcript expression values were modeled and normalized using the Robust Multi-array average (RMA) method, and log2 transformed (AffyPLM, R Bioconductor). Transcripts differentially expressed between animals infected with different viral constructs were identified by a moderated Student’s t-test (limma, R Bioconductor). Only on […]

library_books

Adjuvant Associated Peripheral Blood mRNA Profiles and Kinetics Induced by the Adjuvanted Recombinant Protein Candidate Tuberculosis Vaccine M72/AS01 in Bacillus Calmette–Guérin Vaccinated Adults

2018
Front Immunol
PMCID: 5879450
PMID: 29632533
DOI: 10.3389/fimmu.2018.00564

[…] The raw microarray data were normalized via GeneChip-Robust Multiarray Averaging (GC-RMA) (), and outliers were excluded using the AffyPLM software package (open source; www.bioconductor.org, WA, USA) (–). For the PBMC samples, 4/54 microarrays were excluded, and for WB samples, 11/125 microarrays were excluded based on the relat […]

library_books

The drought tolerant Solanum pennellii regulates leaf water loss and induces genes involved in amino acid and ethylene/jasmonate metabolism under dehydration

2018
Sci Rep
PMCID: 5809557
PMID: 29434236
DOI: 10.1038/s41598-018-21187-2

[…] software. The differences of scaling factor among the different samples did not exceed 3 in any case, so we conclude the results are sufficiently homogenous and feasible as required. The BioConductor affyPLM package was used to obtain Normalized Unsealed Standard Error (NUSE) plot to study the quality of the chips for each set of probes from intensity values of each probeset. All samples presented […]

library_books

Identification and validation of the role of matrix metalloproteinase 1 in cervical cancer

2018
PMCID: 5843389
PMID: 29436615
DOI: 10.3892/ijo.2018.4267

[…] ,) of Bioconductor () (version 3.4) was applied in RStudio (RStudio, Inc., Boston, MA, USA; version 3.3.2) to screen out the DEGs. The raw gene expression profiles of GSE9750 were read using package 'affyPLM' (), and probe quality control was determined by relative logarithmic expression. Following preprocessing of the data by log scale robust multi-array analysis and filling the missing values us […]

library_books

The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes

2018
Sci Rep
PMCID: 5789081
PMID: 29379070
DOI: 10.1038/s41598-018-20104-x

[…] Transcripts in the mouse4302 Affymetrix array were pre-processed (background correction and normalization) using Robust Multi-array Average (RMA) algorithm implemented in the affyPLM, package from bioconductor. […]

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