What is Normalization method used in Deseq2 galaxy


What is the normalization method used in Deseq2 in galaxy.eu exactly ?
I mean RPKM or TPM ?
Could some one please explain .\


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Hi Amir,

Take a look at this post and the links that it has.

Hope this helps,
Dave C

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Thank you for your response.
But i have been searching into galaxy for more detail of normalization method used in deseq2 in galaxy and found this :
DESeq2 normalization

-Objective: Obtain comparable counts between samples, whatever the difference of their libraries sequencing depth

-Accepted values: NGS counts (positive integers ; no missing values)

(null values, will stay null after transformation)

-Range of values: Input: [0;100.000] / Output: [0; 100.000]

-Adapted for: Differential analysis

But i didnt understand it well.
When they ask me what is was your normalization method in your analysis?? Still dont know what to answer

Really need some help on this

Hi @amir,

the normalization method used by Deseq2 is called DESeq2’s median of ratios . This method relies on the calculation of size factors (s), whose objective is to render counts from different samples, which may have been sequenced to different depths, comparable. Herein lies the importance of normalization performed by Deseq2. Deseq2 normalized values are the result of dividing the raw counts by sample’s normalization factor (size factor, s).

You can find an extended explanation here .