Package: arrayMvout 1.70.0

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_1.70.0.tar.gz
arrayMvout_1.70.0.zip(r-4.7)arrayMvout_1.70.0.zip(r-4.6)arrayMvout_1.70.0.zip(r-4.5)
arrayMvout_1.70.0.tgz(r-4.6-any)arrayMvout_1.70.0.tgz(r-4.5-any)
arrayMvout_1.70.0.tar.gz(r-4.7-any)arrayMvout_1.70.0.tar.gz(r-4.6-any)
arrayMvout_1.70.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
arrayMvout/json (API)

# Install 'arrayMvout' in R:

install.packages('arrayMvout', repos = c('https://bioc-release.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-1.71.0(bioc 3.24)arrayMvout-1.70.0(bioc 3.23)

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

infrastructure microarray qualitycontrol

3.82 score 11 scripts 3 mentions 3 exports 162 dependencies

Last updated from:5586fa4089 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	402
linux-devel-x86_64	NOTE	475
source / vignettes	OK	484
linux-release-x86_64	NOTE	596
macos-release-arm64	NOTE	280
macos-oldrel-arm64	NOTE	394
windows-devel	NOTE	452
windows-release	NOTE	473
windows-oldrel	NOTE	438
wasm-release	OK	364

Exports:ArrayOutliers plot show

Dependencies:abind affy affyContam affydata affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr cluster codetools cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr farver fastmap FDb.InfiniumMethylation.hg19 filelock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread 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 nleqslv nlme nor1mix openssl org.Hs.eg.db parody pillar pkgconfig 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 S7 scales scrime selectr Seqinfo 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

arrayMvout -- multivariate outlier algorithm for expression arrays

Introduction | Illustration with MAQC data | Illustration with arrays from a clinical trial network | Manual work with the MAQC subset | Intensity contamination in the spikein data | Appendix: Sources and text for statically computed sections with eval set to false

Rendered fromarrayMvout.Rnwusingutils::Sweave

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