Starting from a reshaped data frame in the correct format, construct an ExpressionSet object that can be used with MIMOSA.
a data.frame that is in the correct form
the indices of the columns that identify features.
The featureCols will be used to construct feature names, and these columns will be dropped from the exprs matrix. The column names are assumed to have names that contain '_' characters separating phenotypic characteristics. These would be generated automatically if the data frame was constrcuted with 'reshape'. They are used to construct the phenoData for the expression set
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E<-ConstructMIMOSAExpressionSet(ICS, reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'), other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'), default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET, .variables=.(TCELLSUBSET,CYTOKINE,UID), featureCols=1,ref.append.replace='_REF')
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