Package: arrayMvout 1.65.0

V. Carey

arrayMvout: multivariate outlier detection for expression array QA

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate

Authors:Z. Gao, A. Asare, R. Wang, V. Carey

arrayMvout_1.65.0.tar.gz
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arrayMvout_1.65.0.tgz(r-4.4-any)arrayMvout_1.65.0.tgz(r-4.3-any)
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arrayMvout.pdf |arrayMvout.html✨
arrayMvout/json (API)

# Install 'arrayMvout' in R:

install.packages('arrayMvout', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

afxsubDEG - Multivariate outlier detection based on PCA of QA statistics
fig3map - Multivariate outlier detection based on PCA of QA statistics
ilmQA - Multivariate outlier detection based on PCA of QA statistics
itnQA - Multivariate outlier detection based on PCA of QA statistics
maqcQA - Multivariate outlier detection based on PCA of QA statistics
s12cDEG - Multivariate outlier detection based on PCA of QA statistics
spikQA - Multivariate outlier detection based on PCA of QA statistics

On BioConductor:arrayMvout-1.63.0(bioc 3.20)arrayMvout-1.62.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructure microarray qualitycontrol

3.34 score 11 scripts 386 downloads 3 exports 161 dependencies

Last updated 21 days agofrom:18d30256e2. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:ArrayOutliers plot show

Dependencies:abind affy affyContam affydata affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi farver fastmap FDb.InfiniumMethylation.hg19 foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable HDF5Array hms httr httr2 illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust mdqc memoise methylumi mgcv mime minfi multtest munsell nleqslv nlme nor1mix openssl org.Hs.eg.db parody pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scales scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml zlibbioc

arrayMvout -- multivariate outlier algorithm for expression arrays

Rendered fromarrayMvout.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2020-12-08
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Multivariate outlier detection based on PCA of QA statistics	afxsubDEG afxsubQC ArrayOutliers fig3map ILM1 ilmQA itnQA maqcQA s12c s12cDEG s12cQC spikQA
ArrayOutliers - wrapper for platform-specific multivariate outlier detection for expression arrays	ArrayOutliers,AffyBatch,numeric,ANY-method ArrayOutliers,ANY,missing,missing-method ArrayOutliers,data.frame,numeric,ANY-method ArrayOutliers,LumiBatch,numeric,ANY-method ArrayOutliers-methods
Class "arrOutStruct" container for ArrayOutliers output	arrOutStruct-class plot,arrOutStruct,ANY-method show,arrOutStruct-method