Question: What are size factors used for in baseMean calculation
0
gravatar for lizzid
29 days ago by
lizzid0
lizzid0 wrote:

I am aware that baseMean is the mean of normalized counts and that normalized counts are calculated by: 1. Taking the mean of a gene across samples 2. Dividing each gene sample by the mean 3. Defining the size factor as the median of the genes divided by the mean

But what exactly is the size factor and what is it used for? It is my understanding that the baseMean corrects issues that arise when very few number of genes are very highly expressed in one condition but not another. Thank you for your help!

deseq2 • 54 views
ADD COMMENTlink modified 29 days ago by Michael Love26k • written 29 days ago by lizzid0
Answer: What are size factors used for in baseMean calculation
0
gravatar for Michael Love
29 days ago by
Michael Love26k
United States
Michael Love26k wrote:

Can you take a look first at the 2014 paper? It explains in full detail these steps.

ADD COMMENTlink written 29 days ago by Michael Love26k

So the raw counts are then divided by the sizing factor?

ADD REPLYlink written 29 days ago by lizzid0

Yes that’s definitely described in the paper also.

ADD REPLYlink written 29 days ago by Michael Love26k
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