Norm.vsn {prot2D} | R Documentation |
This function allows to normalize 2D Gel Volume data using the "Variance Stabilizing Normalization".
Norm.vsn(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 |
The "Variance Stabilizing Normalization" relies on a transformation h, of the parametric form h(x)= arsinh(a+bx) (for details see, Huber et al., 2002). The parameters of h together with those of the calibration between experiments are estimated with a robust variant of maximum-likelihood estimation.This function is based on normalizeVSN
from limma
package.
The function returns a matrix of vsn 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.
Huber, W., Heydebreck, von, A., Sultmann, H., Poustka, A., & Vingron, M. (2002) "Variance stabilization applied to microarray data calibration and to the quantification of differential expression" Bioinformatics, vol. 18 (Suppl 1): S96-S104.
data(pecten) pecten.norm <- Norm.vsn(pecten, n1=6, n2=6, plot=TRUE)