[BioC] DEseq for chip-seq data normalisation

Giuseppe Gallone giuseppe.gallone at dpag.ox.ac.uk
Tue Nov 5 16:32:52 CET 2013


Hi Mike

thanks a lot for this, exactly what I needed.

Best
Giuseppe

On 05/11/2013 13:54, Michael Love wrote:
> hi Giuseppe,
>
> DiffBind calls either edgeR, DESeq or DESeq2 during the processing pipeline.
>
>  From reading the DiffBind 1.8.2 vignette, I see on page 37:
>
>     The final results (as a DESeqDataSet) are accessible within the DBA
>     object as
>     DBA$contrasts[[n]]$DESeq2$DEdata
>     and may be examined and manipulated directly for further customization.
>
>
> So then you can get DESeq2 normalized counts at this point with:
>
> dds <- DBA$contrasts[[n]]$DESeq2$DEdata
> counts(dds, normalized=TRUE)
>
> Mike



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