Introduction | Getting started | Data assumptions | Example of a bad MA plot | Normalizing a data matrix (single assay) | Normalization across multiple assays | Optional arguments | target | maxIterations and precision | Making MA plots | MA plot trick for normalized data | Subsequent Differential Expression Analysis (DEA) | Session info
Package: CONSTANd 1.21.0
Dirk Valkenborg
CONSTANd: Data normalization by matrix raking
Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices.
Authors:
CONSTANd_1.21.0.tar.gz
CONSTANd_1.21.0.zip(r-4.7)CONSTANd_1.21.0.zip(r-4.6)CONSTANd_1.21.0.zip(r-4.5)
CONSTANd_1.21.0.tgz(r-4.6-any)CONSTANd_1.21.0.tgz(r-4.5-any)
CONSTANd_1.21.0.tar.gz(r-4.7-any)CONSTANd_1.21.0.tar.gz(r-4.6-any)
CONSTANd_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CONSTANd/json (API)
| # Install 'CONSTANd' in R: |
| install.packages('CONSTANd', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:CONSTANd-1.21.0(bioc 3.24)CONSTANd-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
massspectrometrycheminformaticsnormalizationpreprocessingdifferentialexpressiongeneticstranscriptomicsproteomics
Last updated from:6cdef6e9cc. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 147 | ||
| linux-devel-x86_64 | NOTE | 172 | ||
| source / vignettes | OK | 173 | ||
| linux-release-x86_64 | NOTE | 145 | ||
| macos-release-arm64 | NOTE | 76 | ||
| macos-oldrel-arm64 | NOTE | 67 | ||
| windows-devel | NOTE | 81 | ||
| windows-release | NOTE | 69 | ||
| windows-oldrel | NOTE | 65 | ||
| wasm-release | OK | 134 |
Exports:CONSTANd
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Data normalization by matrix raking | CONSTANd |
