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

[Gordon K Smyth]

Also see

   ?Tu102

etc.  I agree this could be better sign-posted.

Gordon


On Wed, 4 Jun 2014, Gordon K Smyth wrote:

> 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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