[BioC] Confusion for choosing package for microarray data analysis

[Yi Zou]

Dear list members,

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?

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.

Any answers and suggestions is appreciated

Yi