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  • schaffer
    Member
    • Apr 2009
    • 12
    #1

    RNA-Seq compare edgeR, cufflinks, Partek

    Hi,
    I have compared RNA-Seq in 3 different platforms and get 3 different lists of differential gene expression. Has anyone done this kind of comparison?
    What do you think about this?
    Lana
    Tags: None
  • severin
    Genome Informatics Facility
    • Sep 2009
    • 105
    #2
    how different?

    Are the 3 lists from the same set of data?
    What percentage of genes are the same? different?
    Are the programs using different statistical tests to make the comparisons?
    Do they all incorporate/deal with replicates the same way?
    What are the cutoff p-value used in each? Do they all correct for FDR?

    I would be surprised if you had no genes in common between the three programs.

    Comment

    • mgogol
      Senior Member
      • Mar 2008
      • 197
      #3
      Are there really NO genes in common? Do they share gene ontology terms or pathways?

      Unfortunately, I think it's pretty common in bioinformatics for the analysis techniques to have large effects on the final list of genes and their rank. You could test genes from each list with qpcr to try to see which are the most solid.

      Comment

      • Simon Anders
        Senior Member
        • Feb 2010
        • 995
        #4
        There are a couple of threads that may be of interest, including these:

        huge number of DEGs from cuffdiff - SEQanswers
        http://seqanswers.com/forums/showthread.php?t=12639
        Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)

        Testing/benchmarking RNASeq DE tools - SEQanswers
        http://seqanswers.com/forums/showthread.php?t=10797
        Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

        Comment

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