[BioC] Confusion for choosing package for microarray data analysis

[Vincent Carey 525-2265]

>
> I'm just starting using R to analyze my cDNA microarray data. After a
> few days experience, I found there are so many different packages
> available like marray, limma, sma, com.braju.sma, siggenes...etc. Some
> of them have many functions doing the same work, and definitely each
> package may provide its specific functions. So, I'm a little confused
> for choosing these packages firstly for my following analysis. Hopefully
> experienced members can give me a short answer for these two questions:
>
> 1) Do I have to use these packages together, or just choose one that I
> feel comfortable?

Oftentimes you will need to use several packages to carry
a satisfactory analysis.  The organization of software into packages
is a source of both complexity and flexibility.  A virtue of the
package-based design is that it makes it easier for users to define
their own preferred analysis sequences.  A cost of the package-based
design is that users have to remember both the substantive functions
and the technical organization of functions into packages.  The help.search
function of R can often help in locating a package that addresses
a particular problem.

>
> 2) Can somebody give me a short comparison for those most commonly used
> packages like limma, marray, sma..., especially give me a introduction
> for those specific functions in a package which are not provided in
> other packages? Then I know which package I should choose at beginning.

This is a fair question but it will take considerable work to answer.
We have started on a topical description of packages to replace
the current alphabetic list.  The tasks of defining a partition of
packages across topics, and of eliminating all functional redundancies
among packages, will probably never be completed.  Some very basic
functions that many packages need to use are placed in package Biobase.
This is one effort to reduce redundancies.

Task-oriented documentation is provided in vignettes that are
available with each package: see the first entry in the Documentation
element of the www.bioconductor.org webpage sidebar.  the vExplorer
function of tkWidgets allows you to step through the computations
described in a vignette.