Ok I see. DESeq2 doesn't provide this functionality, sorry! The design
matrix is fixed for all rows/genes.


On Mon, Jun 30, 2014 at 11:59 AM, Jorge Zamora <jz1@sanger.ac.uk> wrote:

> Hello Michael,
>
> For each sample and region I have the percentage homozigosity. I would
> ideally have the formula specified as counts ~ treatment + homozigosity.
>
> Basically I have two variables that are specified per sample and region
> which are the 'counts' (dependent variable) and the 'homozigosity
> percentage' (independent variable), and then I have the 'treatment' which
> depends only on the sample.
>
> I understand I could potentially perform a NB GLM on such dataset but I
> would loose all the features provided by DESeq2.
>
> Any advise will be much appreciated.
>
> Thanks
> Jorge
>
>
>
>
> On 30 Jun 2014, at 16:25, Michael Love <michaelisaiahlove@gmail.com>
> wrote:
>
> hi Jorge,
>
> DESeq2 does not provide functionality to perform modeling with a different
> design matrix for each row (genomic range).
>
> Can you tell us more about the experiment you are trying to analyze?
>
> Section 1.5 is discussing design with multiple factors, e.g.: counts ~
> group + treatment, this is not related to your question I think.
>
> Mike
>
>
> On Mon, Jun 30, 2014 at 11:18 AM, Jorge Zamora <jz1@sanger.ac.uk> wrote:
>
>> Hello,
>>
>> I'm using DESeq2 and I would be interested in specifying continuous
>> independent variables for each sample and genomic range.  I see in section
>> 1.5 (page 10) of the documentation that is possible to associate a given
>> sample with a numeric value. However such values are fixed for all the
>> genomic regions in that sample.
>>
>> Any help will be highly appreciated.
>>
>> Thanks a lot
>> Jorge
>>
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>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose regis...{{dropped:7}}

