User: Roger Vallejo
Roger Vallejo • 120
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Posts by Roger Vallejo
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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 Vallejo • 120
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... 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. ...
written 15.5 years ago by
Roger Vallejo • 120
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... 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 ...
written 15.5 years ago by
Roger Vallejo • 120
• updated
15.5 years ago by
James Wettenhall • 1000
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... 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 Vallejo • 120
• updated
15.5 years ago by
James W. MacDonald ♦ 52k
0
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... 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 ...
written 15.8 years ago by
Roger Vallejo • 120
• updated
15.8 years ago by
James W. MacDonald ♦ 52k
0
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1
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420
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... 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
...
written 15.9 years ago by
Roger Vallejo • 120
• updated
15.9 years ago by
Jeff Gentry • 3.9k
0
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... 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 Vallejo • 120
0
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2
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... 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 ...
written 15.9 years ago by
Roger Vallejo • 120
• updated
15.9 years ago by
Kasper Daniel Hansen • 630
0
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2
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740
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... 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 Vallejo • 120
• updated
16.0 years ago by
James W. MacDonald ♦ 52k
0
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1
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434
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1
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... 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 Vallejo • 120
• updated
16.0 years ago by
James W. MacDonald ♦ 52k
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