Hi!

I am trying to perform a GSEA (Broad Institute) using as input a matrix of normalized protein abundances with 6 conditions (dataset 1) to compare each of them with two custom genesets (based on another protein experiment or dataset 2, from which I took the top upregulated and the top downregulated proteins) to see which of the 6 conditions (phenotypes of dataset 1) is more similar to the signature that I used to create the geneset signature (dataset 2).

Is it possible to put as an input matrix in GSEA (with the appropriate data structure of gene expression matrices like GCT) plus the phenotype matrix and the GMT file with my two genesets to compare each condition of dataset 1 to genesets of dataset 2?

Thank you so much in advance!

Kind regards