[BioC] Targets file, array labels and Limma versions

[Marcus Davy]

Jenny,
help(readTargets) mentions that
 If 'row.names' is null, then the column 'Labels' will
     be used if such exists or, failing that, the column 'FileName'.
This looks like a small typo as the column has to be "Label" not "Labels" in
ReadTargets <- function(){
...
  if ("Label" %in% names(tab)) {
            row.names(tab) <- tab[, "Label"]
        }
...

You can add abbreviated names during file uploading with read.maimages from
a vector or a column of the targets file with the "names" argument.

library(limma)
library(marray)

datadir <- system.file("swirldata", package = "marray")

targets <- readTargets(file.path(datadir, "SwirlSample.txt"))
targets$Label <- c("foo","fodda","fi","fum")

read.maimages(dir(datadir, pattern="spot"), path=datadir, source="spot",
names=targets$Label)
...
An object of class "RGList"
$R
           foo     fodda        fi        fum
[1,] 19538.470 16138.720 2895.1600 14054.5400
[2,] 23619.820 17247.670 2976.6230 20112.2600
[3,] 21579.950 17317.150 2735.6190 12945.8500
[4,]  8905.143  6794.381  318.9524   524.0476
[5,]  8676.095  6043.542  780.6667   304.6190
8443 more rows ...
etc

The assignment of;
colnames(RG) <- targets$Label
Probably doesn't work because the RGList is a list with different types of
structures in it, they do not all have the same column dimensions.

I haven't had any problems under 2.2.0 using limma 2.4.4, not compared to
when R moved from 1.9.1 to 2.0.0 with the addition of "lazy loading" of R
objects.
 
Something maybe of interest to you, biocLite() loads biocinstall.R from
Bioconductor; 
source("http://www.bioconductor.org/scripts/2.2/biocinstall.R")
Looking at the biocinstall script biocLite should be installing the 1.7
stable version of limma (version 2.2.0) but does appear to grabbing the
version 2.4.4, probably for reasons your have already highlighted.

Marcus


On 12/16/05 11:12 AM, "Jenny Drnevich" <drnevich at uiuc.edu> wrote:

> Hi,
> 
> 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?
> 
> Thanks,
> Jenny
> 
> 
>> 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:
>    limma
> "2.4.4"
> 
> 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
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


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