Description Usage Arguments Details Value Author(s) References See Also Examples

This function allows to normalize 2D Gel Volume data using the Quantiles Normalization.

1 |

`data` |
a dataframe of raw 2D Gel Volume data. |

`n1` |
an integer. Number of replicates in condition 1. |

`n2` |
an integer. Number of replicates in condition 2. |

`plot` |
logical. if TRUE (default) displaying two |

2D Gel Volume data must be normalized in order to remove systemic variation prior to data analysis. The principle of the "quantiles normalization" is to set each quantile of each column (i.e. the spots volume data of each gels) to the mean of that quantile across gels. The intention is to make all the normalized columns have the same empirical distribution.This function is based on `normalizeQuantiles`

from `limma`

package.

The function returns a matrix of log2 transformed quantiles normalized data

Sebastien Artigaud sebastien.artigaud@gmx.com

Artigaud, S., Gauthier, O. & Pichereau, V. (2013) "Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools." Bioinformatics, vol.29 (21): 2729-2734.

`normalizeQuantiles`

,`RIplot`

,`ES.prot`

1 2 3 |

```
Loading required package: fdrtool
Loading required package: st
Loading required package: sda
Loading required package: entropy
Loading required package: corpcor
Loading required package: samr
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: Mulcom
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.2-2 (2019-03-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Loading required package: impute
Loading required package: MASS
Loading required package: qvalue
```

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