User: McGee, Monnie

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McGee, Monnie300
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Posts by McGee, Monnie

<prev • 30 results • page 1 of 3 • next >
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Subsetting expression sets for mass spec data - second ask
... 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 ...
classification cancer process written 6.6 years ago by McGee, Monnie300 • updated 6.6 years ago by Sean Davis21k
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Classification in Mass Spectrometry Data
... 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 ...
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(no subject)
... 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 ...
pathways clustering gotools gostats written 10.0 years ago by McGee, Monnie300 • updated 10.0 years ago by anupam sinha270
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Comment: 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, Monnie300
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Comment: 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, Monnie300
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Trouble Loading Rgraphviz in BioC 2.2 and 2.3
... 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 ...
hgu95av2 rgraphviz written 10.7 years ago by McGee, Monnie300
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Mean Plots and Heat Maps for Chromosome Bands
... 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 ...
pathways hgu95av2 written 10.7 years ago by McGee, Monnie300
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Entrez Gene ID to Probe Set Name
... 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 ...
acgh sequencing mirna microarray annotation normalization go preprocessing visualization written 10.7 years ago by McGee, Monnie300 • updated 10.7 years ago by Marc Carlson7.2k
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Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0
... 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 ...
go hgu95av2 biobase annotate written 10.8 years ago by McGee, Monnie300 • updated 10.8 years ago by Marc Carlson7.2k
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Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0
... 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 ...
go hgu95av2 biobase annotate written 10.8 years ago by McGee, Monnie300 • updated 10.8 years ago by Marc Carlson7.2k

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