[BioC] mogene20stcdf

cstrato cstrato at aon.at
Thu May 2 17:30:03 CEST 2013


Dear Nikul,

As Jim mentioned, you could use xps. You can find an example how to 
create the 'scheme' for MoGene 2.0 in ../xps/examples/script4schemes.R. 
However, first you would need to download the library and annotation 
files of MoGene 2.0 from the Affymetrix web-site.
(Furthermore, please read the README file how to install ROOT first.)

Best regards
Christian
_._._._._._._._._._._._._._._._._._
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
_._._._._._._._._._._._._._._._._._



On 5/2/13 3:09 PM, James W. MacDonald wrote:
> Hi Nikul,
>
> You won't be able to use the affy package to process these files.
> Instead you can use either oligo or xps. As for the .db file, those
> files are supplied by Arthur Li, and apparently he hasn't made them for
> the 2.0 series. There is apparently a way to add the annotation to xps,
> but you will have to either look at the help pages or vignettes or wait
> for Christian Stratowa to chime in.
>
> You can also use the AnnotationForge package to create your own .db
> file, but that is a relatively involved process, as the annotation data
> from Affy are not that easy to parse.
>
> Best,
>
> Jim
>
>
>
> On 5/2/2013 6:55 AM, Nikul Soni wrote:
>> Hi all,
>>
>> I am a beginner in R and i use R studio to analyse my mouse liver
>> arrays. I
>> am doing my micro array analysis and it misses cdf environment. I
>> check all
>> the database in R and i cant found for the new chip  Mogene20 and its
>> database i.e. its .db file. is there any possibility that i can
>> download it
>> from other sources.
>>
>> Regards
>> Nikul
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



More information about the Bioconductor mailing list