Hi Naira, Quick question re the CDF. Was this made using TAIR release 8 or release 7 gene set? If 7, do you have any plans to generate one for release 8? Many thanks, Al > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Naira Naouar > Sent: 04 March 2009 08:58 > To: zhen tao > Cc: Bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] How to generate the CDF files for > Arabidopsis TilingArrays > > > Hi Zhen, > > > The Arabidopsis tiling 1.0R cdf that I generated is available > here: ftp://ftp.psb.ugent.be/pub/nanao/athtiling1.0rcdf_1.0.1.tar.gz > > this CDF contains 29670 probesets and was created on a unix > environment. > > If you are analysing tiling arrays in R, you must make sure > that you have enough memory available To make use of the > package those are the instructions: In R: > > library(affy) > library(athtiling1.0rcdf) > data<-ReadAffy() > data at cdfName<-"athtling1.0rcdf" > > Then use rma or mas5 to preprocess your data (gcrma is not > possible because I did not create the probe file). > > Good luck with your analysis. > If you have any problem with the package (installation or > any), feel free to contact me. To install a R package in > unix, : R CMD INSTALL > athtiling1.0rcdf_1.0.1.tar.gz /path/R/libraries > > Best, > Naira > > > zhen tao wrote: > > Dear all, > > > > I'm new to R programming and Bioconductor. Recently I'm trying to > > analyze the data of Arabidopsis Tiling Array using Bioconductor. > > However, I noticed that the CDF files should be included when > > importing the CEL files so that we can do the QC or RMA > studies. But > > there's no cdf/probe package files for this tiling array ( only for > > ATH1). I have downloaded the files named > > attltiling10rattaircdf_10.0.0.tar and > attltiling10rattairprobe_10.0.0.tar > > somewhere. May I know if these files can be used as the > tiling array cdf > > since the R keeps displaying the message > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain At35b_MR_v04 > > Library - package at35bmrv04cdf not installed > > Bioconductor - at35bmrv04cdf not available > > > > If not, is there anyway I can do to generate the cdf file for this > > tiling array? > > > > thanks, > > Tao Zhen > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > ================================================================== > Na?ra Naouar > > Tel:+32 (0)9 331 38 63 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > nanao at psb.vib-ugent.be > http://www.psb.vib-ugent.be > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.