
Thanks for the responses.  I've now got past that hurdle.

Cheers

> Date: Tue, 15 Jun 2010 19:40:23 +0200
> From: cstrato@aon.at
> To: jmacdon@med.umich.edu
> CC: bahhab@hotmail.com; bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] xps - creating ROOT scheme fi les
> 
> Dear Jim,
> 
> Thank you for pointing John to the correct library-files, however I just 
> realized that you mention the design-time annotation files, which are 
> outdated. People should always download the "NetAffx Annotation Files" 
> which contain the latest annotations (currently Release 30).
> 
> Best regards
> Christian
> 
> 
> On 6/15/10 3:10 PM, James W. MacDonald wrote:
> >
> >
> > John Coulthard wrote:
> >> Dear list
> >>
> >> I've got 6x2 Human Exon 1.0 ST arrays to analyse and 3gB of ram so I
> >> believe I need to use xps.
> >> The xps vignette, appendix A.1. says...
> >> "we need to create ROOT scheme files directly from the Aymetrix
> >> source files, which need to be downloaded
> >> first from the Aymetrix web site."
> >>
> >> I think the web page I need to download from is...
> >> http://www.affymetrix.com/browse/products.jsp?productId=131452&navMode=34000&navAction=jump&aId=productsNav#1_3
> >>
> >>
> >> but there is no file that ends with ‘annot.csv’. Should I rename one
> >> of the other annotation files? Which one?
> >
> > How about the one labeled 'HuEx-1_0-st-v2 Annotations, Probeset,
> > Hg18/Build36, CSV (43 MB 10/06/06)', under 'Design Time Annotation Files'?
> >
> >>
> >> The CDF file on this page says 'unsupported' so maybe I should be
> >> looking for CLF-, PGF-files, but they're not on this page either.
> >
> > Yes they are, under the link 'Human Exon 1.0 ST Array Analysis (zip, 131
> > MB)'.
> >
> > Best,
> >
> > Jim
> >
> >
> >>
> >> Can anyone help me out with what to download from where?
> >>
> >> Thanks
> >> John
> >>
> >>
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