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  • umnklang
    Member
    • Oct 2011
    • 16
    #1

    DEGseq calculation method

    I have a question about using DEGseq. I am using it to calculation differentially expressed genes in bacteria. I have Illumina data that I have calculated RPKM from using perl scripts.

    I feed that data into the DEGexp command and set rawCounts=False. I am wondering about the method = "?". Right now I use FET, but I'm not sure at all if this is correct. How does one go about choosing a method?

    -K
    Tags: None
    • wangxj
      Junior Member
      • Sep 2012
      • 7
      #2
      Hello,

      I have the same question:which method should i choose?

      Originally posted by umnklang View Post
      I have a question about using DEGseq. I am using it to calculation differentially expressed genes in bacteria. I have Illumina data that I have calculated RPKM from using perl scripts.

      I feed that data into the DEGexp command and set rawCounts=False. I am wondering about the method = "?". Right now I use FET, but I'm not sure at all if this is correct. How does one go about choosing a method?

      -K

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