Question: What does the relative-log expression normalization mean in the deseq2 wrapper function ?
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gravatar for Aurora
16 months ago by
Aurora10
Aurora10 wrote:

Good morning,

I am trying to understand the relative log expression normalizat

ion made by the DESEQ2 wrapper function.

As far as I understood, It corresponds to the computing of scaling factor as described by Anders and Hubers (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106):

"Hence, to estimate the size factors, we take the median of the ratios of observed counts. Generalizing the procedure just outlined to the case of more than two samples, we use:

sˆj=medianikij(∏mv=1kiv)1/m.

(5)

The denominator of this expression can be interpreted as a pseudo-reference sample obtained by taking the geometric mean across samples. Thus, each size factor estimate sˆj is computed as the median of the ratios of the j-th sample's counts to those of the pseudo-reference."

 

But there is non log transformation in that formula so I'm not sure it is the right description of the RLE normalization method.

 

Thank you for your answers

normalization deseq2 rle • 694 views
ADD COMMENTlink modified 16 months ago by Michael Love25k • written 16 months ago by Aurora10
Answer: What does the relative-log expression normalization mean in the deseq2 wrapper f
0
gravatar for Michael Love
16 months ago by
Michael Love25k
United States
Michael Love25k wrote:

RLE is not terminology created by the DESeq/DESeq2 team.  All you need to know is that   both of these methods use the same normalization and the formula is given in both publications.

ADD COMMENTlink written 16 months ago by Michael Love25k
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