ES.prot {prot2D} | R Documentation |
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.
ES.prot(data, n1, n2, f)
data |
a matrix of spots intensities. |
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. |
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.
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
.
Sebastien Artigaud sebastien.artigaud@gmx.com
Norm.qt
,Norm.vsn
,ExpressionSet
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))