[BioC] xps - creating ROOT scheme fi les

[cstrato]

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outdated.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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>