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  • biofreak
    Member
    • Jun 2011
    • 44
    #1

    limma on log tranformed RPKM values

    Can I run limma on log transformed RPKM values?
    I also ran differential expression analysis using DESeq package (on raw read count data)
    However, the significant genes in both the cases do not match. (very little overlap)
    thanks
    Tags: None
    • dawe
      Senior Member
      • Apr 2009
      • 258
      #2
      According to limma authors, you should not use limma with RPKM, as it will estimate CPM from raw counts...

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