[BioC] Targets file, array labels and Limma versions
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?
R version 2.2.0, 2005-10-06, i386-pc-mingw32
attached base packages:
 "methods" "stats" "graphics" "grDevices" "utils" "datasets"
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
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at uiuc.edu
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