Hi there,

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)
expressionSet <-rma(Data)

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. 

The error actually says something slightly different than what you think. It says it can't find a method for a signature that consists of an ExpressionSet and a character. If you look at the help for gsva(), it says this about the second argument:

gset.idx.list      Gene sets provided either as a list object or as a GeneSetCollection object.

You have to pass in both an ExpressionSet and a list of gene sets, or a GeneSetCollection in order for the function to work. In addition, if you want to use the ssgsea method, you have to use  method = "ssgsea" in your function call. The only time you can use positional argument matching is if you have already passed in objects for the first three arguments as well (e.g., methods is the fourth argument, so R will only know that 'ssgsea' is intended for the fourth argument if there are three arguments ahead of it in the function call).