Hi I've got >Data<-ReadAffy(widget=TRUE) >Data AffyBatch object size of arrays=2560x2560 features (23 kb) cdf=HuEx-1_0-st-v2 (??? affyids) number of samples=18 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) So I'm after huex10stv2cdf But it's not in BioC2.4 or 2.5 but if I search for it on the Bioconductor page it does exist, but I have to log in to get it (password not the subversion password so I can't get)....and it looks old ? huex10stv2cdf [100%] by pkgUp, 2007-05-10 12:55 PM xxx Is it replaced by pd.huex.1.0.st.v2 (which is in a format I'm unfamiliar with)? I can live without it as I guess exonmap can be used but was curious to know where this annotation file is and what vault it is locked in? Paul - Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au

the pd.* pkg is to be used with the oligo package and uses SQLite to store annotation. b On Sep 24, 2009, at 10:59 PM, Paul Leo wrote: > Hi > I've got > >> Data<-ReadAffy(widget=TRUE) > >> Data > AffyBatch object > size of arrays=2560x2560 features (23 kb) > cdf=HuEx-1_0-st-v2 (??? affyids) > number of samples=18 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuEx-1_0-st-v2 > Library - package huex10stv2cdf not installed > Bioconductor - huex10stv2cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > > So I'm after huex10stv2cdf > But it's not in BioC2.4 or 2.5 but if I search for it on the > Bioconductor page it does exist, but I have to log in to get it > (password not the subversion password so I can't get)....and it looks > old ? > huex10stv2cdf [100%] by pkgUp, 2007-05-10 12:55 PM xxx > > > Is it replaced by pd.huex.1.0.st.v2 (which is in a format I'm > unfamiliar with)? > > I can live without it as I guess exonmap can be used but was curious > to > know where this annotation file is and what vault it is locked in? > > Paul > > > - > Dr Paul Leo > Bioinformatician > Diamantina Institute for Cancer, Immunology and Metabolic Medicine > University of Queensland > -------------------------------------------------------------------- ------------------ > Research Wing, Bldg 1 > Princess Alexandria Hospital > Woolloongabba, QLD, 4102 > Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 > Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au > > _______________________________________________ > 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

Hi Paul, The CDF which is commonly expected by exonmap is actually this one: http://xmap.picr.man.ac.uk/download/index#hscdf other details you can probably find in the list archives or just following vignettes and the PLoS One tutorial paper... Cheers, Michal -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Paul Leo Sent: Fri 9/25/2009 3:59 AM To: bioconductor Subject: [BioC] exon array annotation files Hi I've got >Data<-ReadAffy(widget=TRUE) >Data AffyBatch object size of arrays=2560x2560 features (23 kb) cdf=HuEx-1_0-st-v2 (??? affyids) number of samples=18 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) So I'm after huex10stv2cdf But it's not in BioC2.4 or 2.5 but if I search for it on the Bioconductor page it does exist, but I have to log in to get it (password not the subversion password so I can't get)....and it looks old ? huex10stv2cdf [100%] by pkgUp, 2007-05-10 12:55 PM xxx Is it replaced by pd.huex.1.0.st.v2 (which is in a format I'm unfamiliar with)? I can live without it as I guess exonmap can be used but was curious to know where this annotation file is and what vault it is locked in? Paul - Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au _______________________________________________ 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