User: Roger Vallejo

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Roger Vallejo120
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Posts by Roger Vallejo

<prev • 12 results • page 1 of 2 • next >
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Answer: A: RMA vs VSN
... This must be of interest for those preprocessing data from affymetrix chips. We have compared RMA vs VSN performing an lme-ANOVA. If you are wondering what to use RMA or VSN? or what are the potential pitfalls or benefits from using either normalization or background data correction approach. Then, ...
written 15.5 years ago by Roger Vallejo120
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RMA vs VSN
... We have a small experiment with high FDR (around 0.40): 8 affymetrix mouse genechips with 22k genes, 2 replications, saline and E. coli treated mammary tissue, evaluated at 24 hr and 48 hr post injections. I have run both data preprocessing functions via expresso. To subsequenctly run an lme-ANOVA. ...
preprocessing vsn written 15.5 years ago by Roger Vallejo120
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affylmGUI
... I am trying to use affylmGUI in SUN OS 5.8 and did not succeed. I will appreciate some help. I could not get the nice console R window or RGUI after these commands: > library(affylmGUI) > affylmGUI I am using Xterm Exceed. I also installed BWidget and Tktable. I might be missing some oth ...
affylmgui written 15.5 years ago by Roger Vallejo120 • updated 15.5 years ago by James Wettenhall1000
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outliers removal
... Bioconductor Fellows, I have 8 samples (affy arrays with 22,690 probesets). I would like to: 1. Remove outliers and select some genes (using raw signal data from *.CEL files), to then 2. Run the standard data processing technique (let say just RMA) Obviously I have problems on doing these. ...
written 15.5 years ago by Roger Vallejo120 • updated 15.5 years ago by James W. MacDonald52k
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Multtest
... I would like to have an idea on my FDR and I thought that the MULTTEST package will do it. I read the MULTTEST.pdf manual and it is quite clear how to run the golub.RData example file. The problem is on how to run MULTTEST in my arrays data. To begin, how do I make the *.RData file using my data ...
multtest written 15.8 years ago by Roger Vallejo120 • updated 15.8 years ago by James W. MacDonald52k
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package "moe430acdf"
... Lately my R-program is not working properly (Sun Solaris). It used to be easy and smooth. I am using the AFFY mouse expression set 430A and I need to have the package "moe430acdf" in my working directory. I have run this analysis before already without problems. However, lately, it is not loading ...
affy written 15.9 years ago by Roger Vallejo120 • updated 15.9 years ago by Jeff Gentry3.9k
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help loading libraries
... I used to use without any problems the R-1.8.1 package in a SUN Solaris machine. Specifically, I used to call the libraries "affy", "nlme", "cluster" with no problem. However, today I could not call the library "cluster". Why is that? Did we have any major changes on the R program that I am not awar ...
written 15.9 years ago by Roger Vallejo120
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XML installation
... I am trying to install the XML and AnnBuilder packages in a SUN SOLARIS. I have problems installing the XML. I got these error messages (please see below). I can guess that the problem is due to this: checking for xml-config... no checking for xml2-config... no Cannot find xml2-config I wou ...
annbuilder written 15.9 years ago by Roger Vallejo120 • updated 15.9 years ago by Kasper Daniel Hansen630
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R-package installation from source code
... I installed the R-package from source code in a linux readhat 7.3. The program runs. The problem is when I tried to install (or update) new packages and libraries. The new install and libraries goes by default to folders that I have no access (I am not the unix/linux administrator) such as /usr/glob ...
written 16.0 years ago by Roger Vallejo120 • updated 16.0 years ago by James W. MacDonald52k
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R-package binaries install
... I tried to install precompiled binaries to a linux readhat 7.3. At installation, I got this error message (below) [rlv10@lionxl rnew]$ rpm -i R-1.7.1-1.i386.rpm error: cannot get exclusive lock on /var/lib/rpm/Packages error: cannot open Packages index using db3 - Operation not permitted (1) e ...
written 16.0 years ago by Roger Vallejo120 • updated 16.0 years ago by James W. MacDonald52k

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