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Old 02-08-2010, 05:01 AM   #1
Location: Columbus, OH

Join Date: Feb 2009
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Default threshold

In Mortazavi et al (Nature Methods,2008. 5: 621) they used 5 RPMK as threshold and reported genes that had RPMK more than 5.0.
Is this applicable to other experiments or this threshold can be applied to certain experimental values (number of reads, genome size, etc.)?
If 5.0 is not applicable to other experiments, how can I calculate for my particular experiment?

alperyilmaz is offline   Reply With Quote
Old 02-09-2010, 11:09 AM   #2
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Location: Southern France

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i would take a look at the distribution of all RPKM values before setting any threshold
steven is offline   Reply With Quote

rna-seq, threshold

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