, 2007 11:48 AM
To: Vallejo, Roger; r-help@stat.math.ethz.ch
Subject: Re: [R] How to cite the the PDF user's guide for LIMMA
This depends on what style manual you , your
publisher, or your institution uses. One common syle
(APA ) recommends this:
http://library.osu.edu/sites/guides/apagd.php#sid
Dear All,
How to cite the PDF user's guide for the LIMMA package?
This is not about how to cite the LIMMA package.
Roger
Roger L. Vallejo, Ph.D.
Computational Biologist & Geneticist
U.S. Department of Agriculture, ARS
National Center for Cool & Cold Water Aquaculture
11861 Leetown Road
Kearneysvi
Hi Martin,
In using the Cluster Package, I have results for PAM and DIANA
clustering algorithms (below "part" and "hier" objects):
part <- pam(trout, bestk)
# PAM results
hier <- diana(trout)
# DIANA results
GeneNames
Dear R users,
I thought this might be useful for users of the R package HOPACH
(Windows version). Using R 2.4.1 in Windows XP, I found that the
functions: makeoutput, boot2fuzzy and hopach2tree is not recognized by
HOPACH versions 1.4.3 and 1.8.0. However, it works perfect with HOPACH
version 1.6.
Dear R-help,
In performing cluster analysis (packages: hopach, cluster, boot, and
many others), I got these errors:
> makeoutput(kidney, gene.hobj, bobj, file= "kidney.out", gene.names=
gene.acc)
Error: could not find function "makeoutput"
> boot2fuzzy(kidney, bobj, gene.hobj, array.ho
Dear R-Help,
I am using the LIMMA User's Guide 5 January 2007 PDF version. For the
example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I
could not grasp the rationale in developing the contrast.matrix with
these R statements (">" indicates the R command prompt):
> contrast.matr
Dear R-Help,
I am using the function "topTable" from the LIMMA package. To estimate
adjusted P-values there are several options (adjust="fdr" , adjust="BH")
as shown below:
topTable(fit, number = 10, adjust = "BH", fit$Name)
I guess any of these options (fdr, BH, etc.) is using a de
