[BioC] DEseq2 metagenomic analysis without replicates

[Steve Lianoglou]

Hi Kristina,

Just a quick comment regarding your trouble w/ exporting the
regularized data you mention here:


On Mon, Jan 13, 2014 at 11:08 AM, Kristina Fontanez [guest]
<guest at bioconductor.org> wrote:
[snip]

> 2) Normalize count data using a design ~1 option in DEseq2, export normalized counts. As far I can tell - there isn’t a documented procedure to do this in manual, vignettes or on the mailing list. The main problem here is that I can’t figure out a way to export the regularized log transformed counts.
[/snip]

You've already done it.

You are calling `rlogData` on your DESeqDataSet here:

>> Deptreat_rlog=rlogData(Deptreat)
>> dim(Deptreat_rlog)
> [1] 1064   12
>> assay(Deptreat_rlog)
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "missing"’

You are getting an error because Deptreat_rlog is *already* a matrix
of regularized counts (in log2) ... job done ... as in: this is the
matrix you are looking for. See `?rlogData` for more details, but ...
there's not much more to it than that.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech