What are size factors used for in baseMean calculation
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lizzid • 0
@lizzid-22177
Last seen 4.4 years ago

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 • 602 views
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@mikelove
Last seen 22 hours ago
United States

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

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

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Yes that’s definitely described in the paper also.

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