[BioC] Latest Stable Limma Version

[Herve Pages]

Hi Alejandro,

Alejandro wrote:
> Hello,
> I've tried to install the latest stable version of Limma.
> With "biocLite()" command I get Limma 2.9.8 but if I use the 
> "install.package" command I get Limma 2.8.1.
> How can I get the latest "stable" version of Limma package?
> 
> With the following commands I get Limma 2.9.8 (Is it a stable version?)
> 
>     source("http://bioconductor.org/biocLite.R")
>     biocLite(c("limma"))
> 
> With the following command I get Limma 2.8.1
> 
>     install.packages('limma',repos="http://www.bioconductor.org/")


Short answer: I would say that it's probably OK to use limma 2.9.8 with R-2.4
(even if it "looks" like a Bioc devel package).

Long answer:
You've just given us an example of why "dual" hosting of packages can sometimes
lead to confusion. Let me explain: limma is a Bioconductor package but, at the
same time, is hosted on CRAN. The version on CRAN is 2.9.8, but there is no 100%
safe way to know which version of Bioconductor it is supposed to work with.
The middle number in 2.9.8 is odd and, according to Bioconductor version standards,
this suggests a devel (unstable) package. But, since this version is on CRAN, it's
probably the case that the parity of the middle number is irrelevant and that the
package is stable _independently_ of which version of R/BioC you are using.
This is because, generally speaking, CRAN source packages are not tied to a particular
version of R (except of course when they make use of something like "R (>= 2.3.1)"
or "R (<= 2.4.0)" in their Depends field).

So now why do biocLite() and install.packages() pick up a different version of limma?

Officially, the limma package in BioC 1.9 (release) is 2.8.1. That was the latest
available version at the time Bioconductor 1.9 was released back in October 2006.
After a BioC release we create a "release" branch in our Subversion repository so
people can maintain separately the "release" and the "devel" version of their package.
The limma package in the "release" branch has not changed since then and this is the
version you get when you do
  install.packages('limma', repos="http://www.bioconductor.org/")
or
  install.packages('limma', repos="http://bioconductor.org/packages/1.9/bioc")

In the case of the limma package, using biocLite is equivalent to doing
  install.packages('limma',
    repos=c("http://bioconductor.org/packages/1.9/bioc", "http://cran.fhcrc.org/"))
What's happening is that install.packages sees both versions of limma (2.8.1
in http://bioconductor.org/packages/1.9/bioc and 2.9.8 in http://cran.fhcrc.org)
and picks up the higher version (which is probably the right thing to do).

Cheers,
H.


> 
> 
> My R version is 2.4.1.
> 
> Thank you very much,
> Alejandro
> 
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