getMatrixFromExpressionSet {SpeCond} | R Documentation |
getMatrixFromExpressionSet
method returns an matrix of expression values from an ExpressionSet object. It takes into consideration the need of summarizing the samples values by conditions to perform the SpeCond analysis
getMatrixFromExpressionSet(expSet, condition.factor = NULL, condition.method = c("mean", "median","max"))
expSet |
an ExpressionSet object |
condition.factor |
a factor object of length equal to the number of columns (samples) of the ExpressionSet object specifying which sample(s) belong to which condition (condition.factor levels); can be extracted from the phenoData |
condition.method |
the method (mean, median or max) to summarise the samples by conditions (defined by the condition.factor vector) |
For each level of the condition.factor, the expression values of the ExpressionSet object are computed using the condition.method method. If there is only one sample for a condition the expression value is not changed if condition.factor is NULL, the expression matrix of the ExpressionSet object will simply be extracted using exprs()
A matrix of expression values of size (number of row in the ExpressionSet * number of level of the condition.factor)
Florence Cavalli, florence@ebi.ac.uk
Biobase
SpeCond
library(SpeCond) data(expSetSpeCondExample) expSetSpeCondExample f_Tissues=factor(paste("Tissue_",rep(1:32,each=2),sep="")) f_Tissues Mexp=getMatrixFromExpressionSet(expSetSpeCondExample, condition.factor=f_Tissues,condition.method="mean") ## or Mexp=getMatrixFromExpressionSet(expSetSpeCondExample, condition.factor=expSetSpeCondExample$Tissue,condition.method="mean")