Question: edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?
0
gravatar for Gordon Smyth
5.1 years ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Gordon Smyth37k
Answer: edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?
0
gravatar for Gordon Smyth
5.1 years ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:
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 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 5.1 years ago by Gordon Smyth37k
Hi Gordon, thank you, I appreciate your getting back to me so quickly. Regards, 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 On Tue, Jun 3, 2014 at 6:44 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > 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 >> >> > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}
ADD REPLYlink written 5.1 years ago by Lisette de Pillis20
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