voom protocols

voom specifications

Information


Unique identifier OMICS_15212
Name voom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Requirements limma, edgeR, baySeq, DESeq, DSS, PoissonSeq, tweeDEseqCountData
Source code URL http://bioinf.wehi.edu.au/voom/Simulation_Full.R
Maintained Yes

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Maintainer


  • person_outline Gordon Smyth <>

Publication for voom

voom IN pipelines

 (13)
2018
PMCID: 5856766
PMID: 29549264
DOI: 10.1038/s41467-018-03567-4

[…] in cufflinks46, and filtering for long non-coding genes and pairwise differential expression analysis performed in cuffdiff46. data from female mice were analyzed as per hodes et al. 5 whereby the voom47 and limma48 packages were utilized to generate differential expression signatures. for both sexes, differential expression comparisons were generated to compare the effects of esr1 […]

2017
PMCID: 5380837
PMID: 28377524
DOI: 10.1128/mBio.00029-17

[…] per million in at least two of the samples, were removed. quantile normalization (76) was applied, followed by log2 transformation of the counts per million and mean-variance adjustment using the voom program (77)., pca and pearson correlation-based heat maps created using the base r princomp and gplots heatmap.2 functions, respectively, were used to determine the similarity between samples […]

2017
PMCID: 5429854
PMID: 28420881
DOI: 10.1038/s41598-017-00852-y

[…] to the human genome (grch38) using star aligner47. the number of mapped read-pairs were counted using cufflinks based on the gencode v23 annotation48. the raw read counts were transformed using voom49, 50, tmm-normalized51 and qc-analysed using the arrayqualitymetrics package in bioconductor52. samples were scored based on 3 parameters: maplot, boxplot, heatmap. a sample was classified […]

2017
PMCID: 5633036
PMID: 29018623
DOI: 10.7717/peerj.3890

[…] continuous scale using this mean and variance relationship. since plda1 and nblda are count-based classifiers, the transformations are not applied for these classifiers. voomdda classifiers use the voom method inside the algorithm for transformation. a power transformation is applied for plda2 classifier. the rlog transformation is performed for other classifiers, due to its capability […]

2017
PMCID: 5701248
PMID: 29176703
DOI: 10.1038/s41467-017-01877-7

[…] ‘classic’ as the enrichment statistic. for nsd1 wild-type scchn tumors, to evaluate whether nsd1 gene expression was associated with survival differences in laryngeal or oral cancer cases, we used voom-normalized45 rsem (rna-seq by expectation maximization) expression data. nsd1 expression was trichotomized into low (<or = 15% quantile), intermediate (>15% and <85% quantile), or high […]

voom institution(s)
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia

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