Prepare the GCT gene expression file such that identifiers are in the form of Ensembl IDs, but without the version suffix, e.g., ENSG00000139618. For RNA-Seq data, you will need normalize and filter out low count measurements, and perform other preprocessing as needed. Consult your local bioinformatician for help if unsure. Load the GCT and corresponding CLS files into GSEA. Choose gene sets to test—we usually recommend starting with the Hallmarks collection. Choose the CHIP file that matches the identifiers in the GCT file: - Human_ENSEMBL_Gene_ID_MSigDB.vX.chip => Ensembl ID prefix ENSG - Mouse_ENSEMBL_Gene_ID_MSigDB.vX.chip => Ensembl ID prefix ENSMUSG - Rat_ENSEMBL_Gene_ID_MSigDB.vX.chip => Ensembl ID prefix ENSRNOG
Prepare the GCT gene expression file such that identifiers are in the form of Ensembl IDs, but without the version suffix, e.g., ENSG00000139618. For RNA-Seq data, you will need normalize and filter out low count measurements, and perform other preprocessing as needed. Consult your local bioinformatician for help if unsure. Load the GCT and corresponding CLS files into GSEA. Choose gene sets to test—we usually recommend starting with the Hallmarks collection. Choose the CHIP file that matches the identifiers in the GCT file: - Human_ENSEMBL_Gene_ID_MSigDB.vX.chip => Ensembl ID prefix ENSG - Mouse_ENSEMBL_Gene_ID_MSigDB.vX.chip => Ensembl ID prefix ENSMUSG - Rat_ENSEMBL_Gene_ID_MSigDB.vX.chip => Ensembl ID prefix ENSRNOG