[BioC] exon array annotation files

Michal Okoniewski michal.okoniewski at fgcz.ethz.ch
Fri Sep 25 08:24:12 CEST 2009

Hi Paul,

The CDF which is commonly expected by exonmap is actually this one:

other details you can probably find in the list archives or just following vignettes
and the PLoS One tutorial paper...


-----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
I've got 


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?


Dr Paul Leo
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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