[BioC] affy annotation database

[James W. MacDonald]

Hi Paul,

I would recommend switching to either the oligo or xps package for 
analyzing these data. The affy package was never intended to be used 
with the random primer Affy arrays, whereas oligo and xps are.

Best,

Jim



On 1/21/2013 5:13 PM, Paul Rigor wrote:
> Hello,
> I'm using the affy package for the first time. However, the current version
> of the affy package doesn't include  Affymetrix's MoGene cluster annotation
> version 2.0. Could you please point out the correct way of re-constructing
> the annotation packing using the original annotation from the
> manufacturer's site? For example, the current version throws the following
> error message:
>
> *Produces the following error:
>
> *
> *background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoGene-2_0-st
> Library - package mogene20stcdf not installed
> Bioconductor - mogene20stcdf not available*
>
>
> I'd appreciate any help and thank you for your time.
>
> Best,
> Paul
>
>
> --
> Paul Rigor
> http://www.ics.uci.edu/~prigor
>
>
> On Mon, Jan 21, 2013 at 8:00 AM, Rafael Irizarry<rairizarry at gmail.com>wrote:
>
>> Paul, Please send this to the Bioconductor mailing list
>>
>> On Sun, Jan 20, 2013 at 3:11 PM, Paul Rigor<paul.rigor at uci.edu>  wrote:
>>> Hello,
>>> I'm using the affy package for the first time. However, the current
>> version
>>> of the affy package doesn't include  Affymetrix's MoGene cluster
>> annotation
>>> version 2.0. Could you please point out the correct way of
>> re-constructing
>>> the annotation packing using the original annotation from the
>> manufacturer's
>>> site? For example, the current version throws the following error
>> message:
>>> Produces the following error:
>>>
>>> background correction: mas
>>> PM/MM correction : mas
>>> expression values: mas
>>> background correcting...Error in getCdfInfo(object) :
>>>   Could not obtain CDF environment, problems encountered:
>>> Specified environment does not contain MoGene-2_0-st
>>> Library - package mogene20stcdf not installed
>>> Bioconductor - mogene20stcdf not available
>>>
>>>
>>> I'd appreciate any help and thank you for your time.
>>>
>>> Best,
>>> Paul
>>>
>>> --
>>> Paul Rigor
>>> http://www.ics.uci.edu/~prigor
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099