[BioC] Regarding CDF file

[James W. MacDonald]

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]]
>
>         _______________________________________________
>         Bioconductor mailing list
>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>         https://stat.ethz.ch/mailman/listinfo/bioconductor
>         Search the archives:
>         http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>     -- 
>     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

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099