problem in creating ranked list for GSEApreranked gene enrichment

Question

[Ranan Jyoti Sarma]

I did cuffdiff analysis for my RNASeq data Now i want to use GSEAPreranked gene enrichment how to prepare inputfiles for GSEAPreranked analysis from cuffdiff output data.

[Kevin Blighe]

Which GSEA implementation are you using? - e.g., R, JAVA? For preparation of input, generally, take a look here: A: Running GSEA for DEGs

[sarath07bio]

Hi Kevin I am using Java based GSEA gene enrichment. i just want to known how to prepare the rank list from cuffdiff output.

[Kevin Blighe]

I do not believe there is any tutorial specifically for converting CuffDiff output to GSEA input. Please just take a look at the required input for GSEA and then have a think about how you can modify your CuffDiff data. In the thread to which I link in my comment ( A: Running GSEA for DEGs ), I was also using the JAVA-based GSEA program.