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  • wmseq
    Member
    • May 2011
    • 71
    #1

    seq pathway analysis

    Hi every one,
    I am new to the rnaseq pathway analysis. I have finished rnaseq analysis of my experiments, I'd like to do the pathway analysis of de. genes using gage, but I don't know how to start this analysis.

    Can I directedly used the differently expressed genes from rnaseq analysis?

    Thanks!

    Richard
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      RNA-Seq Pathway and Gene-set Analysis Workflows in R/Bioconductor with GAGE/Pathview - SEQanswers
      http://seqanswers.com/forums/showthread.php?t=34679
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


      See tutorials referred to in post #1.
      Last edited by GenoMax; 11-15-2013, 10:39 AM.

        Comment

        • wmseq
          Member
          • May 2011
          • 71
          #3
          Thanks a lot, GenoMax!
          I have read the tutorials, but I have no idea how to start this analysis, because I don't know which results of edger analysis should be feed into GAGE/Pahview for pathway analysis or visualization.

            Comment

            • wmseq
              Member
              • May 2011
              • 71
              #4
              Hi, GenoMax,
              I found the paragraph on jointing workflows with edge R. Thans!

                Comment

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