[BioC] Human Gene 1.1 ST cdf

[cstrato]

Dear Nicolas,

If you want to use xps for Gene 1.1 ST arrays depends on you.

Some people consider it as an advantage that xps uses the official 
Affymetrix PGF-files and annotation files, and the fact that it allows 
to do the analysis on computers with 1-2 GB RAM only. Furthermore, xps 
does not only allow you to use RMA but also MAS5 for these arrays, and 
it supports DABG detection calls.

Best regards
Christian
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On 3/21/11 5:51 PM, Nicolas Servant wrote:
> 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
>>>
>>
>
>