[BioC] DiffBind time course

Rory Stark Rory.Stark at cruk.cam.ac.uk
Tue Sep 9 15:43:54 CEST 2014

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.


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
>	<CAO22HXcAQM_61p7uH4KSKkM13yFn5G5hp7fZS32+cBGTNnpzDw at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>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().
>Enrico Ferrero

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