[BioC] Regarding CDF file

[cstrato]

Dear Deepika,

As Jim kindly mentioned, for xps you need to install ROOT first.
Could you please show your sessionInfo() so that I know which OS you are 
using, so that I can tell you which version of ROOT to install.

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
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On 5/29/13 4:16 PM, James W. MacDonald wrote:
> Hi Deepika,
>
> Please don't take things off-list (e.g., use reply-all when responding).
>
> On 5/29/2013 12:11 AM, deepika lakhwani wrote:
>> Thanks for your advice..
>> I am using R 2.15 version so xps is not working on it. Suggest me xps
>> is better than oligo or not.
>
> I don't know if xps is better than oligo or not. I suspect they are
> roughly comparable, although I have no experience with xps other than
> trying to install it back when installing ROOT on Windows was more
> difficult than it appears to be these days. I will say that xps has been
> around for a long time, and most certainly can be installed using R-2.15.
>
> You do need to install ROOT first. See the README that comes with the
> package:
>
> http://bioconductor.org/packages/release/bioc/readmes/xps/README
>
> Best,
>
> Jim
>
>
>>
>>
>> On Tue, May 28, 2013 at 8:59 PM, James W. MacDonald <jmacdon at uw.edu
>> <mailto:jmacdon at uw.edu>> wrote:
>>
>>     Hi Deepika,
>>
>>
>>     On 5/28/2013 9:58 AM, deepika lakhwani wrote:
>>
>>         Dear Sir,
>>
>>         I have arabidopsis cel files and for differential expression
>>         analysis, i am
>>         using AffylmGUI package but its not running because
>>         AraGene-1_0-st CDF file
>>         is not available on
>>         http://www.bioconductor.org/data/metaData.html site and
>>         when i downloaded the data from affymetrix site, there are so
>>         many files
>>         such as PGF, CLF, QCC files in it but no CDF files. what
>>         should i do ?
>>         Please suggest me. Can you upload the AraGene-1_0-st CDF file
>>         or is there
>>         any other solution for it.
>>
>>
>>     You should be processing these arrays using either oligo or xps.
>>     If you use oligo, the correct file will automatically be
>>     downloaded for you.
>>
>>     Best,
>>
>>     Jim
>>
>>
>>
>>
>>
>>
>>         ThankingYou
>>
>>
>>
>>         regards
>>         Deepika
>>
>>                 [[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
>>
>> regards
>> deepika
>