Question

Is possible to recreate RNASeq count dataset from a dataset normalized with FPKM ?

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5.7 years ago

elmahy2005 ▴ 150

Given a dataset of RNA-Seq expression values normalized with the FPKM method, Is it possible to restore the original count dataset or create a new dataset that behaves very similar to the original count matrix (i.e. we can use in Poisson distribution based models)?

FPKM RNA-Seq • 1.1k views

ADD COMMENT • link updated 5.7 years ago by h.mon 35k • written 5.7 years ago by elmahy2005 ▴ 150

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Unfortunately, it is not possible to calculate raw counts from RPKM data. Best is to start with bam files, and use a program such as featureCounts to generate raw counts.

ADD REPLY • link 5.7 years ago by Benn 8.3k

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Agree on this, because after normalization who knows how the original values were modified.

ADD REPLY • link 5.7 years ago by JC 13k

score 2 · Answer 1 · 2019-02-15

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5.7 years ago

h.mon 35k

If you have the library sizes and effective transcript lengths, you can calculate the original counts. If you have the FPKMs alone, you can't. See the formula for FPKM (from What the FPKM? A review of RNA-Seq expression units):

$FPKM$

ADD COMMENT • link 5.7 years ago by h.mon 35k