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  • 0 value in RPKM (RNA-seq)

    Hi everybody,

    Question about RPKM=0 on RNA-seq analysis.

    Could you tell me how you guys are handling 0 value of RPKM when you count it in a calculation of fold changes.
    For example, when RPKM data of sample A vs. sample B is 100 vs. 0, respectively, it is difficult get the fold change value between sample A and sample B, right? (because it's going to be zero, anyway).

    It could be three ways as follows:
    1) ignore the genes with 0 RPKM from consideration.
    2) genes with 0 RPKM are assigned a inverse value of infinity.
    3) genes with 0 RPKM are assigned a certain small value, e.g., 0.002 (see the following paper: Rowley et al. 2011 Blood 118: e101-11).

    Which way is common (or your preference) and reliable to obtain real fold changes? Or is there any other ways?

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