User: McGee, Monnie
McGee, Monnie • 300
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Posts by McGee, Monnie
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Dear BioC Users,
I would like to be able to subset a mass spectrometry data set by the
biomarkers that were chosen as
important biomarkers. I followed the code in the PROcess vignette to
obtain the biomarkers as follows:
testNorm is a normalized matrix of m/z values from 253 samples
> bmkfile ...
written 6.6 years ago by
McGee, Monnie • 300
• updated
6.6 years ago by
Sean Davis ♦ 21k
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... Dear List,
I am new to the analysis of Mass Spectrometry data. In particular, I
am using SELDI-TOF data.
I have used the package PROcess to analyze the ovarian cancer data
found in Petricoin, et. al. (2004),
as found in http://home.ccr.cancer.gov/ncifdaproteomics/ppatterns.asp.
I was hoping to us ...
written 6.7 years ago by
McGee, Monnie • 300
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Dear Anupam,
I am responding to you message about finding signaling pathways to
which a list of over/under expressed genes belong.
There are several tools for this: Reactome, OntoExpress, PathExpress,
CLASSIFI (requires clustering of the genes using some type of
clustering tool before use).
Most ...
written 10.0 years ago by
McGee, Monnie • 300
• updated
10.0 years ago by
anupam sinha • 270
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C: (no subject)
... Dear Martin,
Thanks for your help. It seems to me that both Rgraphviz and Graphviz
must be compiled from source code, at least, that's what the README
file leads me to believe. I don't suppose that anyone out there knows
how to get Rgraphviz working using binaries?
Anyway, I search my computer f ...
written 10.7 years ago by
McGee, Monnie • 300
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C: (no subject)
... Dear Martin,
Thank you. What are the steps for Macintosh? I've copied in the
error and my sessionInfo below.
As far as I can tell, the version of Graphviz that I downloaded for
the Mac (Version 2.20 (2.20.3)) does not have a README file. Do I
need to download that from the Graphviz website, als ...
written 10.7 years ago by
McGee, Monnie • 300
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... Dear BioC Group,
I am trying to load Rgraphviz but I keep receiving an error. I have
installed graphviz 2.2. I searched the mailing list archives, and, as
far as I can tell, no error like this has appeared. I tried loading
Rgraphviz on two different computers running two different versions of
R ...
written 10.7 years ago by
McGee, Monnie • 300
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... Dear BioC Users,
I am following the code for Chapter 13 of "Bioconductor Case Studies"
(dealing with GSEA. The example of GSEA analysis in the text shows
the use of KEGG pathways to determine gene sets. Then the functions
KEGGmnplot and KEGGheatmap are used to obtain a mean plot and a heat
map fo ...
written 10.7 years ago by
McGee, Monnie • 300
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... Here is the previous query with a more descriptive subject.
-----Original Message-----
From: McGee, Monnie
Sent: Thu 10/23/2008 11:14 AM
To: bioconductor at stat.math.ethz.ch
Subject: RE: Bioconductor Digest, Vol 68, Issue 23
Dear List,
Is there an elegant way to obtain the name of a probe set f ...
written 10.7 years ago by
McGee, Monnie • 300
• updated
10.7 years ago by
Marc Carlson • 7.2k
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... Dear Mark,
Thank you.
I don't have access to the source tree. Does this mean that I need to
download the annotate library again, or can I grab the functions
separately? If the latter, how is that done?
Best,
Monnie
Monnie McGee, Ph.D.
Associate Professor
Department of Statistical Science
Sout ...
written 10.8 years ago by
McGee, Monnie • 300
• updated
10.8 years ago by
Marc Carlson • 7.2k
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... Dear List,
I was going through the examples in the query documentation (written
in June of 2008) for the annotate package when I came to an error.
The function "locuslinkQuery" no longer seems to exist, and neither
does "locuslinkByID". Here are my code and session info:
> sessionInfo()
R ve ...
written 10.8 years ago by
McGee, Monnie • 300
• updated
10.8 years ago by
Marc Carlson • 7.2k
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