Question: Is possible to recreate RNASeq count dataset from a dataset normalized with FPKM ?
1
gravatar for elmahy2005
15 months ago by
elmahy200580
elmahy200580 wrote:

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)?

rna-seq fpkm • 347 views
ADD COMMENTlink modified 15 months ago by h.mon29k • written 15 months ago by elmahy200580
3

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 REPLYlink written 15 months ago by Benn8.0k
1

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

ADD REPLYlink written 15 months ago by JC10k
2
gravatar for h.mon
15 months ago by
h.mon29k
Brazil
h.mon29k wrote:

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 COMMENTlink modified 15 months ago • written 15 months ago by h.mon29k
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