[BioC] exon array annotation files

[Benilton Carvalho]

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
>
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