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Old 02-14-2012, 10:54 AM   #1
cuekt
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Location: Columbia, MO, USA

Join Date: Feb 2012
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Default 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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