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pcaMethods specifications

Information


Unique identifier OMICS_14344
Name pcaMethods
Alternative name principal component analysisMethods
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An ExprSet object or a numerical matrix.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.72.0
Stability Stable
Requirements
methods, BiocGenerics, Biobase, lattice, ggplot2, MASS, matrixStats, Rcpp(>=0.11.3)
Maintained Yes

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No version available

Documentation


Maintainer


  • person_outline Henning Redestig

Publication for principal component analysisMethods

pcaMethods citations

 (31)
library_books

Missing Value Imputation Approach for Mass Spectrometry based Metabolomics Data

2018
Sci Rep
PMCID: 5766532
PMID: 29330539
DOI: 10.1038/s41598-017-19120-0

[…] ertain convergence threshold. In metabolomics data, we scaled and centralized the data matrix first and then applied this imputation approach with the number of PCs setting to five by using R package pcaMethods.Mean: This method replaces missing elements with an average value of non-missing elements in the corresponding variable.Median: This method replaces missing elements with a median value of […]

library_books

Characterization of the Primary Metabolome of Brachystegia boehmii and Colophospermum mopane under Different Fire Regimes in Miombo and Mopane African Woodlands

2017
Front Plant Sci
PMCID: 5735074
PMID: 29312388
DOI: 10.3389/fpls.2017.02130

[…] (FDR) correction (Supplementary File ). Principle Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA) and Heatmap plots were obtained in the R software using the packages: pcamethods (), mixOmics () and pheatmap (). […]

library_books

Single cell RNA sequencing uncovers transcriptional states and fate decisions in haematopoiesis

2017
Nat Commun
PMCID: 5725498
PMID: 29229905
DOI: 10.1038/s41467-017-02305-6

[…] genes using ERCCs as spike-in in all 1422 blood cells. We used the scLVM R package (version 0.99.2) to identify the 1845 most highly variable genes (Supplementary Fig. ).Principal component analysis (pcaMethods (version 1.64.0)), independent component analysis (FastICA (version 1.2) and diffusion maps (destiny (version 1.3.4)) were used to verify that all cells were intermixed in the reconstructed […]

call_split

Metabolite and transcript markers for the prediction of potato drought tolerance

2017
Plant Biotechnol J
PMCID: 5866952
PMID: 28929574
DOI: 10.1111/pbi.12840
call_split See protocol

[…] ls (high, medium and low) based on tertiles of the probability distribution.Missing values in the metabolite (5.5%) and transcript (2.2%) data were estimated by PCA using the Nipals method (R‐package pcaMethods; Stacklies et al., ).For drought tolerance prediction by Random Forest models, data from the experimental field trials were used as a training set, while samples of 16 independent agronomic […]

call_split

Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production

2017
PLoS One
PMCID: 5560702
PMID: 28817696
DOI: 10.1371/journal.pone.0183504
call_split See protocol

[…] ddition, a principal component analysis (PCA) [] was performed, based on the molecular similarity matrix, in order to infer the population structure in the sweet sorghum accessions, using the package pcaMethods for the R software [], available at the Bioconductor software []. […]

library_books

Molecular signatures reflecting microenvironmental metabolism and chemotherapy induced immunogenic cell death in colorectal liver metastases

2017
Oncotarget
PMCID: 5652706
PMID: 29100312
DOI: 10.18632/oncotarget.19350

[…] for calculations.Gene expression data was log2-transformed and quantile normalized using the LIMMA []. Imputation of missing values was performed by local least squares (llsImpute from the R package pcaMethods []) with k=20. For subgroup discovery and visualization, data were assessed using a two-way, unsupervised average linkage hierarchical clustering on genes showing high overall variability ( […]

Citations

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pcaMethods institution(s)
CAS-MPG Partner Institute for Computational Biology, Shanghai, China; Max Planck Institute of Molecular Plant Physiology, Postdam, Germany; Ernst-Moritz-Arndt-University of Greifswald, Competence Center for Functional Genomics, Greifswald, Germany; University of Potsdam, Potsdam, Germany

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