[BioC] DEseq2 metagenomic analysis without replicates
lianoglou.steve at gene.com
Mon Jan 13 20:29:10 CET 2014
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:
> 2) Normalize count data using a design ~1 option in DEseq2, export normalized counts. As far I can tell - there isnâ€™t a documented procedure to do this in manual, vignettes or on the mailing list. The main problem here is that I canâ€™t figure out a way to export the regularized log transformed counts.
You've already done it.
You are calling `rlogData` on your DESeqDataSet here:
>  1064 12
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function â€˜assayâ€™ for signature â€˜"matrix", "missing"â€™
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.
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