I am trying to do gene set variance analysis using GSVA package for different samples. I have a list of signification genes as ExpressionSet and a GeneSet
> eset<-new("ExpressionSet",exprs=as.matrix(scaledcounts)) > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 25658 features, 21 samples element names: exprs : none phenoData: none featureData: none experimentData: use 'experimentData(object)' Annotation: none
and my Gene list is
which I am conversiting to a GeneSet
I am getting the following error message, which I am failing to understand with my limited knowledge in oo programming.
`gsva<-gsva(eset,HpoGS) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘gsva’ for signature ‘"ExpressionSet", "GeneSet", "missing"’
I am wondering does it have anything to do with the way, I am creating the expressionSet or GeneSet? Any help to address this would be highly appreciated. Thanks a lot in advance!