I am trying to get the ssgsea algorithm running that is in the gsva package. I am reading an affymatrix dataset for this, convert it to an ExpressionSet object and then run the function. However, I get this error :
allFiles <- list.files('./affymatrix/TisMix_WTGene1_CEL/',full.names=TRUE,pattern = "\\.CEL$")
Data<-ReadAffy(filenames = allFiles)
result <- gsva(expressionSet,'ssgsea')
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘gsva’ for signature ‘"ExpressionSet", "character"’
Any ideas? GSVA documentation says it can be an expressionSet.