[BioC] Targets file, array labels and Limma versions

Jenny Drnevich drnevich at uiuc.edu
Thu Dec 15 23:12:57 CET 2005


I have a 3 questions that are somewhat related:

I noticed a discrepancy between the Limma vignette (21 Nov 2005) and 
readTargets() in Limma 2.4.4 (complete sessionInfo at the end). In the 
vignette on pg. 12, it says you can put a "Name" column in your Targets.txt 
file to give a shorter label for output, graphs, etc. However, when I did 
this and called readTargets(), the rownames of the targets object were the 
longer file names. Looking at the code for readTargets, it appears the 
column has to be called "Label", not "Name"?

I am also having troubles getting shorter labels for my RGlist. It would be 
great if read.maimages() could get both the FileNames and Name/Label info 
from a targets= option, or alternatively have a colnames= option where 
targets$Label could be plugged in. However, I thought it could be done 
manually using colnames(RG), but I'm getting the following error message:

 > colnames(RG) <- targets$Label
Error in "colnames<-"(`*tmp*`, value = c("a1", "a2", "a3", "a4", "a5",  :
         'dimnames' applied to non-array

colnames(RG) does give a character vector of the names, so why it doesn't 
work for assignment?

This may or may not have something to do with the version of Limma... which 
leads me to my last question: Why does the development version of Limma get 
installed when using biocLite() ? (haven't checked getBioC)  I've seen that 
Gordon has said he doesn't keep "stable" and "developmental" versions like 
other maintainers and wants everyone to use the most recent version, so 
perhaps this is why. However, I keep getting a warning message when I load 
Limma that it was built under R 2.3.0. Do you anticipate there being any 
problems with using Limma 2.4.4 under R 2.2.0? I suspect that there won't 
be any real problems, but I want to point out that these warning messages 
can be be disconcerting to R novices - I just taught a workshop on R and 
Bioconductor and had to answer this question many times. If the newest 
version of Limma is likely to be continually built under the developmental 
version of R instead of the recommended stable version of R,  perhaps a 
note explaining the situation could be put in the vignette or somewhere else?


 > sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

other attached packages:

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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