[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:
https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-August/002180.html
The data also used to be on the GEO database with the accession names
given, but was removed in 2009.
Best wishes
Gordon
------- 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
Mathematics
Department of Mathematics
Harvey Mudd College
Claremont, CA 91711
909-621-8975
www.math.hmc.edu/~depillis
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