| 24 | | 1. Create a two column file with gene names as first column and numeric values for second column (eg. log FC), does not need to be sorted and it should have extension ".rnk". |
| 25 | | * Assigning weights: There is no standard way to assign weights, however, it should reflect some logical order. GSEA uses the correlation between expression and phenotype to assign weights, if the list is not pre-ordered or ranked. A similar scheme can be used to rank genes by log2 ratio, t-statistic, or a scoring scheme that takes into account both log ratio and p-value. |
| 26 | | * If a gene list is not unique, duplicate genes can be given a //shared// weight, for eg. if a gene occurs four times in the list it is given a weight of 0.25, if it is unique a weight of 1 is given. |
| 27 | | 2. Run GSEA: Tools -> GseaPreranked |
| | 24 | 1. Create a two column file with gene names as first column and numeric values for second column (eg. log2 fold change, log2 ratio). The file does not need to be sorted and it should have extension ".rnk". |
| | 25 | * The second column, used to rank genes, could be log2 fold change, t-statistic, or another scoring scheme that takes into account both log ratio and p-value. |
| | 26 | 2. To run using the GUI |
| | 27 | * 1. Upload your ranked file "file.rnk". Click on "Steps in GSEA analysis -> Load data" |
| | 28 | * 2. Click on "Tools -> GseaPreranked" |
| | 29 | * 3. Select one of the gene sets from the "Gene sets database". We recommend starting with the Hallmarks set (h.all). You can find more information about the sets [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|here ]]. |
| | 30 | * 4. Click on "Tools -> GseaPreranked" |
