[BioC] DESeq counts normalized option fails

[Simon Anders]

On 09/30/2011 03:36 PM, Jane Charlesworth wrote:
> Hi,
> I'm new to using DESeq and managed to get my data into a CountDataSet object
> okay. I can figure out how to generate normalised counts by myself, but when
> I try to set the argument to the count accessor function as described in the
> documentation, it fails and gives the following message:
>
>> counts( "EC1_2_countDataSet", normalized=TRUE)
> Error in counts("EC1_2_countDataSet", normalized = TRUE) :
>    unused argument(s) (normalized = TRUE)
>
> If I look at the man page for "counts" it doesn't list any arguments - could
> it be that I'm using an obsolete version of DESeq?

The 'normalized' option is only available in the devel version of DESeq.

In the release version, you need to write:
   t(t(counts(cds))/sizefactors(cds))

  S