exon array annotation files
2
0
Entering edit mode
Paul Leo ▴ 970
@paul-leo-2092
Last seen 9.6 years ago
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
Annotation Cancer cdf exonmap Annotation Cancer cdf exonmap • 1.1k views
ADD COMMENT
0
Entering edit mode
@benilton-carvalho-1375
Last seen 4.0 years ago
Brazil/Campinas/UNICAMP
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
ADD COMMENT
0
Entering edit mode
@michal-okoniewski-2676
Last seen 9.6 years ago
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
ADD COMMENT

Login before adding your answer.

Traffic: 808 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6