[BioC] How to output Normalised count data from DESeq?

[Wolfgang Huber]

Hi Fabrice,

you can use

	counts(x, normalized=TRUE)

For more info, have a look at the manual page of the 'counts' accessor 
function.

	Best wishes
	Wolfgang


Aug/17/11 9:25 AM, Andreia Fonseca scripsit::
> Hi Fabrice,
>
> when you use DESeq after normalizing you get the size factors. I think that
> if you divide your count data by the size factor you get the normalized
> count.
> Kind regards,
> Andreia
>
> On Wed, Aug 17, 2011 at 12:29 AM, Fabrice Tourre<fabrice.ciup at gmail.com>wrote:
>
>> Dear list,
>>
>> I have got the raw counts for each exon using HTSeq-count.
>> I want to use DESeq to normalise the counts. How can I output the
>> Normalised count data from DESeq?
>>
>> Thank you
>>
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>
>
>


-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber