Question: Raw expression data is better for FPKM normalised expression profile in RNA seq
1
gravatar for enterid
3.0 years ago by
enterid10
enterid10 wrote:

I am working on the Differential Expression Analysis on RNA-Seq Data between tumor sample and normal sample, while my lecturer suggest me better use the raw expression data instead of using FPKM as expression unit , anyone could tell me why ? or what is the advantage for this ?

rna-seq • 995 views
ADD COMMENTlink modified 2.0 years ago by swbarnes27.5k • written 3.0 years ago by enterid10
3
gravatar for Antonio R. Franco
3.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.4k wrote:

If you want further details, you can visit Joshua Starmer youtube collection of videos

In this one, you can see details about how DESeq2 normalize RNA-Seq data from raw data

And in this one, how does it edgeR

ADD COMMENTlink written 3.0 years ago by Antonio R. Franco4.4k
2
gravatar for Asaf
3.0 years ago by
Asaf7.2k
Israel
Asaf7.2k wrote:

In a nutshell, because you'll be able to apply statistical models to your values. When you normalize to FPKM you lose your ability to do so and end up with less robust statistical tests

ADD COMMENTlink written 3.0 years ago by Asaf7.2k

alright , thank you

ADD REPLYlink written 3.0 years ago by enterid10

If an answer was helpful you should upvote it. If the answer resolved your question too, you should mark it as accepted.

ADD REPLYlink written 3.0 years ago by WouterDeCoster43k
1
gravatar for swbarnes2
2.0 years ago by
swbarnes27.5k
United States
swbarnes27.5k wrote:

The short answer is...the statisticians who wrote the software to do differential expression analysis have thought a lot about how best to normalize, and you should just let them do it. Those softwares all want raw counts as input so they can normalize, you should give them that, and let them do their thing. If you know what you are doing, and have compelling reasons to apply a different normalization function, the softwares have ways to allow you to do that, but a simple FPKM method is not going to be better than what the authors of the software have worked out.

ADD COMMENTlink written 2.0 years ago by swbarnes27.5k
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