[BioC] DEseq for chip-seq data normalisation
giuseppe.gallone at dpag.ox.ac.uk
Tue Nov 5 16:32:52 CET 2013
thanks a lot for this, exactly what I needed.
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
> 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)
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