affyPLM protocols

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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

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affyPLM in pipelines

 (32)
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 […]

2017
PMCID: 5268451
PMID: 28125591
DOI: 10.1371/journal.pone.0169223

[…] pass the stringent model based quality control assessment of affymetrix genechips, which was carried out using the corresponding affyplm package (https://bioconductor.org/packages/release/bioc/html/affyplm.html). briefly, the normalized unscaled standard errors (nuse) function was run over the data. this process accounts for differences in variability between genes based on standard error (se) […]

2017
PMCID: 5331713
PMID: 28245863
DOI: 10.1186/s13075-017-1237-9

[…] robust multiarray average (rma) in the affy package (version 1.36.1). array quality was assessed by computing relative log expression (rle) and normalized unscaled standard error (nuse) using the affyplm package (version 1.34.0). differential expression was assessed using the moderated (empirical bayesian) t test implemented in the limma package (version 3.14.4). correction for multiple […]

2017
PMCID: 5493306
PMID: 28665939
DOI: 10.1371/journal.pone.0179797

[…] neuroscience institute (brainarray) at the university of michigan. array quality was assessed by computing relative log expression (rle) and normalized unscaled standard error (nuse) using the affyplm bioconductor package (version 1.34.0) []. moderated t tests were performed using the limma package (version 3.14.4). correction for multiple hypothesis testing was accomplished using […]

2017
PMCID: 5581396
PMID: 28894456
DOI: 10.3389/fpls.2017.01464

[…] and normalization/summarization of all cel files were performed using r, the bioconductor (), and a robust multi-chip average (rma) (; ). the quality of the genechip data was assessed using the affyplm package (). the annotation of each gene in the csv file ath1-121501.na31.annot.csv (downloaded in april 2012) released by affymetrix was used. for stress treatment- and genotype comparison, […]


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affyPLM in publications

 (171)
PMCID: 5893559
PMID: 29636452
DOI: 10.1038/s41467-018-03762-3

[…] discordant arrays were excluded from further downstream analyses., 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). […]

PMCID: 5879450
PMID: 29632533
DOI: 10.3389/fimmu.2018.00564

[…] probe sets derived from gene transcripts (affymetrix, oh, usa)., 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 […]

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

[…] 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 […]

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 […]

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

[…] downstream analysis., 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., all differential expression analysis was performed using the two-sided moderated t-test implemented in limma package. correction for multiple hypothesis testing […]


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