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  • cummeRbund getSig(): alpha?

    I've used the following command to extract significant genes:

    mySigGenes <- getSig(cuff, alpha = 0.05, level = "genes")

    However, I don't understand why terms familiar to me such as "FPKM" and "q-value" are not arguments in this filtering process. Also, what does "alpha" mean?

  • #2
    P-value http://en.wikipedia.org/wiki/P-value.

    Comment


    • #3
      Ah, I see. So alpha is the cutoff for the p-value then. Does the same apply for q-value as well?

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