I am pretty new to bioinformatics; I am doing an immunology research project in which I am learning how to use R. I am now supposed to use the DOSE package from BioConductor to analyse a dataset downloaded from an interaction network I created on STRING with a list of selected proteins.
I have been asked to filter the genes by NORMALISED ENRICHMENT SCORE (NES) with the DOSE package but I have no idea on how to obtain it with the data downloaded from STRING, because NES is not included anywhere in the excel files I downloaded and imported from STRING (the ones containing the interaction networks between my list of proteins, the file found underneath the "clusters" option).
What I am trying to obtain from this is a list with the proteins which are most repeated in the pathway list obtained from STRING ("Biological Process", "WikiPathways", etc.), but I am a bit confused on how to get them.
Does anyone know how to do it?