Package: ffpe 1.57.0

Levi Waldron

ffpe: Quality assessment and control for FFPE microarray expression data

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Authors:Levi Waldron

ffpe_1.57.0.tar.gz
ffpe_1.57.0.zip(r-4.7)ffpe_1.57.0.zip(r-4.6)ffpe_1.57.0.zip(r-4.5)
ffpe_1.57.0.tgz(r-4.6-any)ffpe_1.57.0.tgz(r-4.5-any)
ffpe_1.57.0.tar.gz(r-4.7-any)ffpe_1.57.0.tar.gz(r-4.6-any)
ffpe_1.57.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ffpe/json (API)

# Install 'ffpe' in R:

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

On BioConductor:ffpe-1.57.0(bioc 3.24)ffpe-1.56.0(bioc 3.23)

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

microarray geneexpression qualitycontrol

4.12 score 33 scripts 424 downloads 2 mentions 3 exports 162 dependencies

Last updated from:d854178d4f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	308
linux-devel-x86_64	NOTE	540
source / vignettes	OK	524
linux-release-x86_64	NOTE	623
macos-release-arm64	NOTE	466
macos-oldrel-arm64	NOTE	287
windows-devel	NOTE	491
windows-release	NOTE	419
windows-oldrel	NOTE	506
wasm-release	OK	285

Exports:CATplot sampleQC sortedIqrPlot

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr 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 memoise methylumi mgcv mime minfi multtest nleqslv nlme nor1mix openssl org.Hs.eg.db 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 sfsmisc siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TTR TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable xts XVector yaml zoo

ffpe package user guide

Rendered fromffpe.Rnwusingutils::Sweaveon Jun 04 2026.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Quality assessment and control for FFPE microarray expression data	ffpe-package ffpe
Make a Concordance at the Top plot.	CATplot
Sample quality control for FFPE expression data	sampleQC sampleQC,AffyBatch-method sampleQC,LumiBatch-method sampleQC,matrix-method sampleQC-method
Minimal box plot of samples, which get ordered optionally by batch, then by IQR.	sortedIqrPlot sortedIqrPlot,AffyBatch-method sortedIqrPlot,LumiBatch-method sortedIqrPlot,matrix-method