Gene set enrichment Analysis

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6.4 years ago

anitha.b • 0

Hi, I am running GSEA for Gene Ontology(C5), Immunology(C7) and oncology(C6). But i am getting results as a pdfs only for Immunology and Oncology. why i am not getting results for Gene ontology?? (reference organism is HUMAN)

Thank you, Anitha

RNA-Seq genome • 1.4k views

ADD COMMENT • link 6.4 years ago by anitha.b • 0

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Please be more specific, where and how are you running these analyses?

ADD REPLY • link 6.4 years ago by Michael 54k

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Thank you for your reply Michael. I am using GSEA for the annotation of rna seq analysis after completing cuffdiff and i am running analysis in my local system after creating .cls and .txt file. (.txt file from raw counts)

Thanks Anitha

ADD REPLY • link 6.4 years ago by anitha.b • 0

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Please do not add an answer which should be a comment, use add comment for that. Besides, it is not clear what 'running GSEA' means as there are many tools that can do this, web-tools, R-packages, the 'official' GSEA tool from Broad http://software.broadinstitute.org/gsea/index.jsp. As you are referring to Immunology, etc. I assume it is GSEA/MSigDB.

Then we possibly need to see an example dataset as well. It might be possible that your input genes are either not recognized or lack annotation in the database. If you provide a reproducible example, someone might be able to help.