[BioC] DESeq: normalizing additional sample to already normalized set of samples

[Dorota Herman]

hi Mike,

thanks a lot! That is what I have been looking for

Dorota


Michael Love wrote:
> hi Dorota,
>
> I don't know if you are using DESeq or DESeq2, but in the latter I 
> have added an argument geoMeans to estimateSizeFactors which allows 
> you to provide the geometric means from a previous dataset to 
> normalize a new one. See the Examples section for ?estimateSizeFactors 
> for DESeq2 v1.2
>
> Mike
>
>
> On Thu, Nov 21, 2013 at 6:24 AM, Dorota Herman 
> <dorota.herman at psb.vib-ugent.be 
> <mailto:dorota.herman at psb.vib-ugent.be>> wrote:
>
>     Hello everyone,
>
>     I have a question regarding normalization for a library size in
>     DESeq. I have a set of samples, which I had normalized with a
>     function estimateSizeFactors. Is there an option to normalized an
>     additional sample with respect to normalized previously set of
>     samples. I know that in the normalization in EdgeR treats a first
>     sample as a reference by default. How can I do it in DESeq?
>
>     regards
>     Dorota
>
>
>     -- 
>     ==================================================================
>     Dorota Herman, PhD
>     VIB Department of Plant Systems Biology, Ghent University
>     Technologiepark 927
>     9052 Gent, Belgium
>     Tel: +32 (0)9 3313692 <tel:%2B32%20%280%299%203313692>
>     Email:dorota.herman at psb.vib-ugent.be
>     <mailto:Email%3Adorota.herman at psb.vib-ugent.be>
>     Web: http://www.psb.ugent.be
>
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