[BioC] Human Gene 1.1 ST cdf

[Nicolas Servant]

Thanks Jim.
I found a cdf on BrainArray
http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=131554&navAction=jump&aId=productsNav#1_1
Then I plan to simply use the RMA function from the affy package.

require(hugene11stv1hsentrezgcdf)
require(hugene11stv1hsentrezg.db)
require(hugene11stv1hsentrezgprobe)
cdfname <- "hugene11stv1hsentrezg"
abatch <- ReadAffy(celfile.path=rawDataDir, cdfname=cdfname)
rmaData <- rma(abatch, cdfname = cdfname)

Is there still some reason to use xps or oligo instead of the affy
package ?
The vignette of oligo seems to also use RMA ...
http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/doc/V5ExonGene.pdf

Thanks
Nicolas

James W. MacDonald a écrit :
> Hi Nicolas,
>
> On 3/21/2011 11:18 AM, Nicolas Servant wrote:
>> Hi,
>>
>> I'm looking for the cdf package of the Affymetrix Human Gene 1.1 ST
>> ArrayPlate.
>> I found the hugene1.0 package but not the 1.1 (only the annotation
>> package .db are available) ...
>> Does anybody know if such a package exists ?
>
> No. We build the cdf package for this chip (1.0) using the unsupported
> cdf file that affy supplies. They have never to my knowledge offered
> an unsupported version of the 1.1 chip, so we don't have a cdf package.
>
> You can however use some functions from the aroma.affymetrix project
> to create a cdf if you are feeling adventurous
> (https://stat.ethz.ch/pipermail/bioconductor/2010-December/036730.html).
>
> But you should really be using either oligo or xps to analyze these
> chips. The affy package was never intended for these chips, and there
> are real reasons not to use it.
>
> Best,
>
> Jim
>
>
>>
>> Thanks
>> Nicolas
>>
>


-- 
Nicolas Servant
Equipe Bioinformatique
Institut Curie
26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE

Email: Nicolas.Servant at curie.fr
Tel: 01 56 24 69 85
http://bioinfo.curie.fr/