[BioC] where to start?

[Sean Davis]

On Apr 20, 2005, at 1:56 AM, Malik Yousef wrote:

> Hello,
>
> I have a gene expression data set build up form rows of genes  
> expression as
> fellow:
>
> GeneID  GeneName      Sample1    .......... Samplen
>
>  Category                      +1      ...........-1
>
>  1             gene1            0.5 ..............0.67
>
>  2             gene2            0.34 ............. 0.78
>
>
>
> How I could use bioconductor to analyze this data set and get the most
> informative genes, classification.. Clustering and etc
>

Malik,

You will have to decide what specific questions you want to answer  
using your data.  To get a sense of what bioconductor has to offer, try  
looking here:

http://www.bioconductor.org/ 
faq.html#What%20documentation%20exists%20for%20Bioconductor

The vignettes give a lot of detail about how to use different packages.  
  The BioConductor Short Courses are very helpful as a starting place.   
When you run into specific problems, ask here.  If you want more help  
here, you will probably have to be more specific about your data, what  
you have tried, and what hasn't worked.  Single channel or two-color?   
Patient samples or cell lines or something else?  Expression or CGH?   
How many classes of sample?  What are the research  
questions/hypotheses?

Sean