Question: how the data should look like after the normalization
0
gravatar for tonja.r
3.5 years ago by
tonja.r450
UK
tonja.r450 wrote:

I was taught and everywhere in the tutorials is written that after the normalization it is preferable that the curves look the same. However, if we have two conditions, one where is nothing expressed and another where all genes are highly expressed then according to this logic I can lose all significant expressions because the curves will look the same. What should I consider instead? Should be the shape the same and it is ok if the some curves are higher and anthers not? 

Beneath are the square root of the normalized values. The shape is the same, however they are of different height and do not correspond to the initial experiment conditions

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R • 1.1k views
ADD COMMENTlink modified 3.5 years ago by svlachavas560 • written 3.5 years ago by tonja.r450
1

There are a lot of different normalization methods, which one(s) are you referring to. BTW, most methods aren't appropriate to cases where there's a global change in expression.

ADD REPLYlink written 3.5 years ago by Devon Ryan89k

I was looking at the normalization for RNA-seq used by DESeq2 and edger where they correct with the sizeFactors. 

ADD REPLYlink written 3.5 years ago by tonja.r450
0
gravatar for svlachavas
3.5 years ago by
svlachavas560
Greece
svlachavas560 wrote:

Perhaps you could also check the "quantro approach" for the choise of "appropriate" normalization method  

http://www.genomebiology.com/2015/16/1/117

http://www.stephaniehicks.com/quantroPaper/

ADD COMMENTlink written 3.5 years ago by svlachavas560

but what is wrong with this curves? Do they really have to be all the same regarding shape, height?

ADD REPLYlink written 3.5 years ago by tonja.r450
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