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News: J-Express 2011 released. Download from jexpress.bioinfo.no
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Author Topic: HuGene-1_0-st-v1 .r4 .txt/csv  (Read 5307 times)
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« on: February 07, 2013, 07:50:26 PM »

We have been trying to analyze HuGene-1_0-st-v1.r4, and we have some q├╝estions.
I have read that .r3 was the last .CDF, and now is impossible to download the .r4 from Affymetrix.  They give you .r4.all.ps ; .r4.bgp; .r4.clf; .r4.mps; .r4.pgf; .r4.qcc.  I think it's possible to open .CEL with GCOS but, is it possible with j-express? Maybe in a future?

Moreover, fortunately we have .txt with the RMA performed.  But we have some problems trying to perform Gene ontology mapping or GSEA.  I think the problem is that .CSV file from Affymetrix don't have a column with ONLY geneID or other ID, they give for example swissprot and more information after de ID.  I have followed your manual and downloaded daily .obo and daily GO archives, but with or without synonims (col 3 or 11) it is not readable. I'd like to know if I'm doing something wrong or if there is some other .TXT with a compatible annotation.

Thanks for your help.
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