[BioC] edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?

Gordon K Smyth smyth at wehi.EDU.AU
Wed Jun 4 02:57:30 CEST 2014

Dear Professor de Pillis,

The SAGE data is bundled with edgeR, but not by these names.  See:


The data also used to be on the GEO database with the accession names 
given, but was removed in 2009.

Best wishes

------- original message ------------
Tue Jun 3 20:48:26 CEST 2014

Dear edgeR people,

I've just installed edgeR 3.6.2 following the instructions from 
http://www.bioconductor.org/packages/release/bioc/html/edgeR.html and 
downloaded the documentation from that same page.

I would like to follow the example in chapter 4 of the document 
edgeRUsersGuide.pdf "SAGE pro les of normal and tumour tissue", but a web 
search for the files

GSM728.txt, GSM729.txt, GSM755.txt, GSM756.txt

yields no results.  These files do not seem to have come bundled with the 
edgeR package. Could you please point me to where I can find these files?

I am running R 3.0.2 (2013-09-25) on Mac OSX.

Thank you!

L.G. de Pillis, Ph.D.
Norman F. Sprague Jr., Professor of Life Sciences and Professor of
Department of Mathematics
Harvey Mudd College
Claremont, CA 91711

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