Norm.qt {prot2D} | R Documentation |
This function allows to normalize 2D Gel Volume data using the Quantiles Normalization.
Norm.qt(data, n1, n2, plot = T)
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
data(pecten) pecten.norm <- Norm.qt(pecten, n1=6, n2=6, plot=TRUE)