[BioC] DiffBind time course

[Enrico Ferrero]

Hi Rory,

Many thanks for the explanation. At first sight, using a blocking
factor should probably do the job - I hadn't though about it.
For future reference, how and at what step I can extract the binding
matrix or edgeR/DESeq2 objects to continue the analysis with those
packages?

Thanks!
Best,


On 9 September 2014 14:43, Rory Stark <Rory.Stark at cruk.cam.ac.uk> wrote:
> Hello Enrico-
>
> You can do some more advanced modelling using DiffBind, but to really get
> the full power of the GLMs, you probably want to extract the binding
> matrix and/or the edgeR/DESEq2 objects and run the appropriate RNA-seq
> package directly.
>
> Within DiffBind, you can use the "block" parameter in dba.contrast to
> indicate the metadata field that has the timepoint. So if the
> sample/control distinction is indicated as the Treatment and the timepoint
> info is in the Condition, you can say:
>
>> DBA = dba.contrast(DBA,categories=DBA_TREATMENT, block=DBA_CONDITION)
>> DBA = dba.analyze(DBA) # for default edgeR analysis
>
> This will model the data as [~Condition + Treatment] and give you the
> effects of the treatment consistent across timepoints. There are other
> models you may want to fit, (eg [~Condition * Treatment]); for this you
> would need to run edgeR (or DESeq/DESeq2) independently -- their
> respective vignettes give examples of analyzing time series data.
>
> -Rory
>
> On 09/08/2014 12:02, Enrico Ferrero <enricoferrero86 at gmail.com>  wrote:
>
>>
>>----------------------------------------------------------------------
>>
>>Message: 1
>>Date: Mon, 8 Sep 2014 12:01:57 +0100
>>From: Enrico Ferrero <enricoferrero86 at gmail.com>
>>To: "bioconductor at r-project.org" <bioconductor at r-project.org>
>>Subject: [BioC] DiffBind time course
>>Message-ID:
>>       <CAO22HXcAQM_61p7uH4KSKkM13yFn5G5hp7fZS32+cBGTNnpzDw at mail.gmail.com>
>>Content-Type: text/plain; charset=UTF-8
>>
>>Hi,
>>
>>Is there a way to use DiffBind to analyse time course data?
>>I have sample and control replicates at five different time points and
>>I would like to know which sites show differential binding over time.
>>
>>At the moment I'm doing multiple pairwise comparisons (i.e: sample at
>>24h vs control at 24h) and I'm trying to understand if it's possible
>>at all and, if yes, what parameters I should pass to dba.contrast()
>>and dba.analyze().
>>
>>Thanks!
>>
>>--
>>Enrico Ferrero
>



-- 
Enrico Ferrero