Mean/Median-balanced quantile normalization for preprocessing omics data

This package contains a modified quantile normalization (QN) for preprocessing and analysis of omics or other matrix-like organized data with intensity values biased by global, columnwise distortions of intensity mean and scale. The modification balances the mean intensity of features (rows) which are rank invariant (RI) or nearly rank invariant (NRI) across samples (columns) before quantile normalization [1]. This helps to prevent an over-correction of the intensity profiles of RI and NRI features by classical QN and therefore supports the reduction of systematics in downstream analyses. Additional package functions help to detect, identify, and visualize potential RI or NRI features in the data and demonstrate the use of the modification.

To install this package, you need R version >= 3.6.

For installation from Bioconductor run in R:

```
#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
BiocManager::install("MBQN")
```

For installation from Github run in R:

```
# install.packages("devtools")
# devtools::install_github("arianeschad/MBQN")
```

or

```
# install.packages("githubinstall")
# githubinstall::githubinstall("MBQN")
```

The core of the MBQN package uses `normalizeQuantiles()`

from the
package `limma`

[2], available at
https://bioconductor.org/packages/release/bioc/html/limma.html, for
computation of the quantile normalization. Optionally,
`normalize.quantiles()`

from the package `preprocessCore`

[3],
available at
https://bioconductor.org/packages/release/bioc/html/preprocessCore.html,
can be used.

The function `getPXDfile()`

in MBQN uses data from the PRIDE repository.
To run this function one needs the R package `rpx`

[4] to download the
data.

To install these packages in R run:

```
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install(pkgs = c("preprocessCore","limma","rpx","SummarizedExperiment"))
```

Further information about the package is provided at the wiki https://github.com/arianeschad/MBQN/wiki

[1] Brombacher, E., Schad, A., Kreutz, C. (2020). Tail-Robust Quantile Normalization. BioRxiv. [2] Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47. [3] Ben Bolstad (2018). preprocessCore: A collection of pre-processing functions. R package version 1.44.0. https://github.com/bmbolstad/preprocessCore. [4] Laurent Gatto (2019). rpx: R Interface to the ProteomeXchange Repository. R package version 1.18.1. https://github.com/lgatto/rpx.

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