[BioC] exon array annotation files

[Michal Okoniewski]

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 at 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

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