[BioC] Targets file, array labels and Limma versions

Jenny Drnevich drnevich at uiuc.edu
Fri Dec 16 17:01:19 CET 2005

Hi again,

>>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.
>As Marcus Davy has explained, read.maimages() already has such an argument 
>called 'names'.

Oops - missed that! Sorry...

>BTW, I am thinking of allowing the targets frame to be passed directly to 
>read.maimages(), e.g.,
>   RG <- read.maimages(files=targets, source="genepix")
>If 'targets' is a data.frame, then the Filenames and Labels columns of 
>would be used to locate the data files and associated names. Would you 
>find this a useful facility?


>>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.
>This happens because limma is on CRAN as well as on Bioconductor. 
>biocLite() works differently from the older getBioC() script in that it 
>searches CRAN as well as the Bioconductor repositories. It installs the 
>latest version of each package that it can find for the version of R being 
>run. For limma, the latest version will usually be the one on CRAN.
>>  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?
>There are no problems with limma 2.4.4 under R 2.2.0. However, if you are 
>running R 2.2.0, you should never get limma or any other package built for 
>R 2.3.0. I believe the intention is that neither biocLite() nor 
>install.packages() should ever install a package built for a version of R 
>other than that being run by the user. The only way I know of that the 
>user could get limma built for R 2.3.0 would be (i) by actually running R 
>2.3.0 or (ii) by manually downloading the Windows build from 
>http://www.bioconductor.org/download/bioc1.8/. Doing the latter and then 
>installing it in R 2.2.0 would be a user error and would lead to the 
>warning message that you mention.

Ah - that solves the mystery... I didn't know that limma was also on CRAN, 
and that's the version that biocLite() installs. I had been installing R on 
three other computers when I noticed the differences in the limma versions 
and vignettes from when I had installed the newest R & Bioconductor on my 
computer back in October. I assumed they were getting the development 
version, so I downloaded that for my computer so I could get the same 
commands (one default changed somewhere...) and page numbers for my 
workshop. I just downloaded & installed limma 2.4.4 from CRAN, and now it 
loads without the warning.

Thanks so much,

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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