User: Jane Fridlyand

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j****@stat.berkeley.edu

Posts by Jane Fridlyand

<prev • 9 results • page 1 of 1 • next >
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extracting interactions between members of the KEGG pathways
... Hello, I was wondering whether there is an infrastructure in one of the BioC packages to extract connections between members of the KEGG pathways. As far as I can tell KEGG package allows to get the identifiers of the members very easily, however I do not see a way of going one step further so to ...
pathways infrastructure cancer graph written 13.7 years ago by Jane Fridlyand90 • updated 13.7 years ago by rgentleman5.5k
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problems with biomaRt on Mac OS X (10.4.2 = Tiger)
... Dear Mac users: more problems with bioC packages on Mac OSX: this time with biomaRt (R 2.2. and latest BioC release). It installs but then when i am doing martConnect() it complains about MySQL being out of date (but seems to establish connection). I actually downloaded the latest version of MySQL ...
biomart written 14.1 years ago by Jane Fridlyand90
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Comment: C: Rgraphviz load problem
... Dear Mac users can anyone who successfully installed appropriate version of graphviz (v>1.12) and was able to install/load Rgraphviz on MAC OSX share the steps they took with me? I was previously having issues because graphviz version was older but not I am not quite sure. do i need to compile ...
written 14.1 years ago by Jane Fridlyand90
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Answer: A: Rgraphviz load problem
... I am trying to install Rgraphviz under Mac OS X Tiger (10.4.2). I am using the latest R (2.2) and Rgraphviz 1.8 . I downloaded and successfully installed what i think is the most current graphviz dmg for mac (1.10.dmg). It installed in /usr/local/lib/graphviz. I added thje fowllowing to .bashrc: e ...
written 14.1 years ago by Jane Fridlyand90
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biomaRt/RMySQL installation help
... I am trying to install package biomaRt under windows XP. I fetched appropriate versions oDBI and RMySQL from http://stat.bell-labs.com/RS-DBI/download/ and (successfully: no errors) installed them from local zip files. I then installed biomaRt off Bioconductor (1.6 release). However when ...
cancer biomart written 14.3 years ago by Jane Fridlyand90 • updated 14.3 years ago by Seth Falcon7.4k
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SAM in R and normalization question
... Hi, I just recently saw R-function to compute Q-values given unadjusted p-values on John Storey web page: http://www.stat.berkeley.edu/~storey/qvalue/index.html I have not tried it myself. My question concerns normalization discussion on which I have been reading in recent postings. Does anyo ...
normalization written 16.5 years ago by Jane Fridlyand90
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Comment: C: specifying hyperlinks on the plot
... Sorry!: i mean "image= stuff in pdf file": i.e. clicking on the hyperlinked text jane ********************************************************************** **************** Jane Fridlyand, Postdoctoral Scientist UCSF Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N412 Tel: (415 ...
written 17.1 years ago by Jane Fridlyand90
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Comment: C: specifying hyperlinks on the plot
... currently i am specifying clone names with a very small cex size and passing images on the biologists in the pdf format who then open it up in the Photoshop which i guess has a very good ability to zoom in (maybe adobe acrobat does too: i just don't have the full version). In any case focusing the m ...
written 17.1 years ago by Jane Fridlyand90
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specifying hyperlinks on the plot
... Hi, is there a capability in R/bioconductor for specifying hyperlinks from a , say, postscript or pdf plot. For instance, when I produce n by p image matrix with log2ratios and with all the clone names for the columns listed, is there a way to create a mark-up so that by clicking on a clone name to ...
cancer written 17.1 years ago by Jane Fridlyand90 • updated 17.1 years ago by Vincent J. Carey, Jr.6.3k

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