Hello. I am working on an Alzheimer's disease RNA-seq dataset and I calculated the log2 fold change for a number of genes in different samples and wanted to run it on GSEA. According to the steps listed on the GSEA wiki, I used the GSEA-Preranked tool wherein I created a .rnk file with one column as gene symbols and the other with log2 values for each sample, sorted in order of highest to lowest log2 values. I made sure it was tab delimited. GSEA loads this .rnk file successfully but on running the tool shows an error in the results.
I tried running the normal GSEA tool with the RNA-seq counts data instead, along with the .cls and .gct file and the same happens; files are successfully loaded but results show an error. I have previously used GSEA only with microarray data so I could be using the wrong parameters but I can't figure it out. I would really appreciate help with this!
