[BioC] xps - creating ROOT scheme fi les

James W. MacDonald jmacdon at med.umich.edu
Tue Jun 15 15:10:43 CEST 2010

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 



> Can anyone help me out with what to download from where?
> Thanks
> John
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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