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 _._._._._._._._._._._._._._._._._._ 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]] >> >> _______________________________________________ >> 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 >