problem in creating ranked list for GSEApreranked gene enrichment

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4.9 years ago

Ranan Jyoti Sarma ▴ 90

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 • 744 views

ADD COMMENT • link updated 4.9 years ago by sarath07bio • 0 • written 4.9 years ago by Ranan Jyoti Sarma ▴ 90

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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 • link 4.9 years ago by Kevin Blighe 87k

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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 • link 4.9 years ago by sarath07bio • 0

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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 • link 4.9 years ago by Kevin Blighe 87k

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