problem in creating ranked list for GSEApreranked gene enrichment
0
0
Entering edit mode
3.2 years ago

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.

RNA-Seq rna-seq • 515 views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2093 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6