prot2D (version 1.10.0)

ES.prot: Create an ExpressionSet containing 2D Gel Volume Data

Description

This function create an an ExpressionSet containing 2D Gel Volume Data and associated metadata. It requires a matrix of 2D Gel Volume data with Gels as columns and Spots as rows as well as a dataframe describing the data.

Usage

ES.prot(data, n1, n2, f)

Arguments

data

a matrix of spots intensities. data should be intensities displayed with gels as columns with the name of columns corresponding to the names of the gels and spots as rows with the names of the rows corresponding to the name of the spots. The replicates for each condition should be ordered in following columns.

n1

an integer. Number of replicates in condition 1.

n2

an integer. Number of replicates in condition 2.

f

a dataframe giving the factors for data. f dataframe should have only 1 column giving the 2 levels of factor with rownames corresponding to the names of gels (in the same order as data).

Value

The function returns an ExpressionSet. The matrix of spots intensities (i.e. Volume) is stored in the assayData slot of the ExpressionSet and can be retrieved with exprs. In the featureData slot the log2-ratio is computed and can be retrieved with fData.

Details

Usually data matrix should be the output of Norm.qt and therefore is log2-transformed. In data the columns (i.e. Gels) must be ordered with replicates from condition 1 before those from condition 2.

See Also

Norm.qt,Norm.vsn,ExpressionSet

Examples

data(pecten)
data(pecten.fac)

pecten.norm <- Norm.qt(pecten, n1=6, n2=6, plot=TRUE) #Quantiles normalization of the data
ES.p <- ES.prot(pecten.norm, n1=6, n2=6, f=pecten.fac)
head(exprs(ES.p))