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Question: DESeq2 Which gene used to normalize?
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gravatar for michi.s
8 weeks ago by
michi.s0
michi.s0 wrote:

Is it possible to get a function which gives the name of the gene used to normalize?

ADD COMMENTlink modified 8 weeks ago by Steve Lianoglou12k • written 8 weeks ago by michi.s0
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gravatar for Michael Love
8 weeks ago by
Michael Love15k
United States
Michael Love15k wrote:

hi,

Take a look at the original DESeq paper. DESeq2 uses the median ratio method described here for normalization. The default normalization is the estimation of size factors presented in Equation 5. The default size factor estimate uses all of the genes that have positive counts for all samples.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106

ADD COMMENTlink written 8 weeks ago by Michael Love15k

Hi Michael,

thank you for the fast reply. I now the method, but my point is, if I take the median of ratios to the geometric mean, then there is in fact for each sample one gene I normalize to (or two genes, if the total number of genes is even). This information could be really helpful for explaining biologists what happened to their data...

ADD REPLYlink written 8 weeks ago by michi.s0
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gravatar for Steve Lianoglou
8 weeks ago by
Genentech
Steve Lianoglou12k wrote:

Unless you specify a set of control genes to use, every gene which has all-non-zero-observations is used.

See the help inĀ ?estimateSizeFactors and ?estimateSizeFactorsForMatrix for more information.

ADD COMMENTlink written 8 weeks ago by Steve Lianoglou12k
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