[BioC] Human Gene 1.1 ST cdf

cstrato cstrato at aon.at
Mon Mar 21 19:48:54 CET 2011


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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C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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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
>>>
>>
>
>



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