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ffpe

Quality assessment and control for FFPE microarray expression data


Bioconductor version: Release (3.18)

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).

Author: Levi Waldron

Maintainer: Levi Waldron <lwaldron.research at gmail.com>

Citation (from within R, enter citation("ffpe")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ffpe")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ffpe")
ffpe package user guide PDF R Script
Reference Manual PDF

Details

biocViews GeneExpression, Microarray, QualityControl, Software
Version 1.46.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License GPL (>2)
Depends R (>= 2.10.0), TTR, methods
Imports Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
System Requirements
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Suggests genefilter, ffpeExampleData
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ffpe_1.46.0.tar.gz
Windows Binary ffpe_1.46.0.zip
macOS Binary (x86_64) ffpe_1.46.0.tgz
macOS Binary (arm64) ffpe_1.46.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ffpe
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ffpe
Bioc Package Browser https://code.bioconductor.org/browse/ffpe/
Package Short Url https://bioconductor.org/packages/ffpe/
Package Downloads Report Download Stats