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Qvalue specifications


Unique identifier OMICS_00624
Name Qvalue
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.12.0
Stability Stable
grid, splines, ggplot2, R(>=2.10), knitr, reshape2
Maintained Yes


No version available


Publication for Qvalue

Qvalue citations


Control procedures and estimators of the false discovery rate and their application in low dimensional settings: an empirical investigation

BMC Bioinformatics
PMCID: 5833079
PMID: 29499647
DOI: 10.1186/s12859-018-2081-x

[…] R packages are available for all described control methods via CRAN [] or Bioconductor []. Specifically, we used the packages multtest [], qvalue [] (Bioconductor), mutoss [] and fdrtool [] (CRAN) in our study. We applied the methods using default options of the packages. However, Storey’s q-value application displayed an error whenever […]


A Genome Wide Search for Gene Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG

Front Genet
PMCID: 5834486
PMID: 29535761
DOI: 10.3389/fgene.2018.00060

[…] separately for the analysis of each exposure. To control the false discovery rate, we used the method described by Storey and Tibshirani () where q-values are computed from the p-values. The function qvalue from the R-package “q-value” in the Bioconductor repository [https://www.bioconductor.org/, Gentleman et al., ] was used to generate the q-values. A low q-value indicates a low likelihood that […]


Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan

Sci Rep
PMCID: 5758520
PMID: 29311585
DOI: 10.1038/s41598-017-18391-x

[…] ng SPSS version 22.0 statistical software (IBM Corp., Armonk, NY, USA). Intergroup differences were analysed using Mann-Whitney U test, followed by FDR calculation on R software (ver. 3.3.0) with the qvalue package (http://www.bioconductor.org/packages/release/bioc/html/qvalue.html) (n = 1,538). Correlation analysis was performed by Spearman’s correlation coefficient (n = 113). For all statements, […]


Intraspecific variation in response to magnitude and frequency of freeze thaw cycles in a temperate grass

PMCID: 5751040
PMID: 29308126
DOI: 10.1093/aobpla/plx068

[…] ently square-root transformed for the ANOVA analyses (non-transformed values are shown in the figures). All analyses were performed using R 3.4.3 (), installing additional ‘raster’ (), ‘heplots’ (), ‘qvalue’ () and ‘rgdal’ packages (). […]


Variants in the CNR1 gene predispose to headache with nausea in the presence of life stress

PMCID: 5347942
PMID: 27762084
DOI: 10.1111/gbb.12352

[…] ssing data. To adjust P values for the multiple testing false discovery rate q values were calculated and were accepted at level of 5% (Q value, http://www.bioconductor.org/packages/release/bioc/html/qvalue.html). To handle possible ancestral differences, ethnicity was determined by the self‐reported data derived from the Background questionnaire (see Questionnaires) and subjects with European whi […]


Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA Seq in non heading Chinese cabbage

BMC Genomics
PMCID: 4840866
PMID: 27103267
DOI: 10.1186/s12864-016-2625-2

[…] le : Figure S11a).In addition, we mapped DEGs to terms in KEGG database to identify significantly enriched pathways. Among the mapped pathways, 20, 11, 22, and 5 pathways were significantly enriched (Qvalue < 0.01) under 4, 0, -4, and 44 °C treatments, respectively (Additional file : Figure S12, Table S9). Notably, common enrichments were observed in photosynthesis pathway, metabolic pathway, and […]

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