[BioC] Installation Problems

[Steve Lianoglou]

Hi Rishi,

Please use "reply all" when replying to emails on the list so that discussion stays on the list. This way you will likely get better help since more eyeballs are looking at your problems, and the list can be used as a resource for people in the future.

On May 23, 2013, at 1:37 PM, RISHI SINHA <rishi.z.sinha at berkeley.edu> wrote:

> Hi Steve,
> 
> Sorry, I guess I really don't know exactly what I'm downloading from Bioconductor. I'm using a book, Applied Statistics for Bioinformatics Using R, and it says:
> "Bioconductor is primarily based on R and can be installed, as
> follows.
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite()"

Ahh, I see. The packages that get installed by default have likely changed since that book was published. Still, you can likely broadly apply much of what's there, although you may run into bumps.

The `biocLite()` function installs thing from bioconductor's repositories. You can use it to specify packages you'd like, so you could do:

R> source("http://bioconductor.org/biocLite.R")
R> biocLite("multtest")
R> library(multtest)
R> library(golub)

and you can continue on your way, you will like need to install some other things. I suspect installing "limma" depends on enough other things that it should get you on your way:

R> biocLite("limma")

> I don't think I skipped any steps according to the book, but if there are any intermediate steps I missed, that would be nice to know.

You haven't skipped anything it seems, but the world of bioconductor (and the defaults) has moved on since that book was published in 2009 .. I guess you are using this one, right?

http://cran.r-project.org/doc/contrib/Krijnen-IntroBioInfStatistics.pdf

I've never read that particular work, but I'd suggest as you go through it and new packages are introduced, I'd go here:

http://bioconductor.org/packages/release/BiocViews.html#___Software

to find the package (if it's a bioconductor one). Click through to the package's main page, install it via the instructions you see there, and read the vignettes that it comes with (under the "Documentation" section) before continuing with the book.

Have fun,

-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech