[BioC] Gene Selection

[Heike Pospisil]

Dear Naomi (and Stephen)

thanks for your replies. Sorry for the little information I gave in my 
last email.

I have 79 cel-files. Each chip is classified concerning three different 
criteria (categories). For each category, there exist at least 3 subclasses:

               Cat.A                       Cat.B                         
  Cat.C
1.CEL     g                                  l                           
         n
2.CEL     n                                  
0                                   r
3.CEL     r                                   
n                                   l
...
79.CEL   n                                   r 
                                   0
          ---------                    ----------                      
----------
          3 subclasses             4 subclasses                  4 
subclasses
          n,g,r                         
l,0,n,r                            l,0,n,r

For the first analysis, I only need to select differential expressed 
genes for one category.

I read some tutorials and could reproduce these analyses, but I am not 
sure what the right strategy for me (limma or multtest or simple ttest 
or whatever).

Thanks for your help and best wishes
Heike

> Dear Dr. Pospisil,
> I am sure someone would be happy to assist you, but we need more 
> information.
>
> How many treatments (conditions, types of tissue, genotype, or whatever)?
> What is the objective of the study: differential expression? gene 
> expression clustering?  predicting tissue type?
>
> --Naomi Altman
>
> At 10:06 AM 2/3/2005, Heike Pospisil wrote:
>
>> Dear users,
>>
>> I am (nearly) a BioC beginner and hope someone could help me with my 
>> first analysis.
>> I am looking for methods to select discriminating genes from a couple 
>> of cel-files using the following metrics: T-statistics, chi-square, 
>> Wilkins' and correlation-based feature selection. I would be glad to 
>> get some hints or links to some tutorials.
>>
>> Thanks in advance,
>> Heike
>>
>> -- 
>> Dr. Heike Pospisil
>> Center for Bioinformatics, University of Hamburg
>> Bundesstrasse 43, 20146 Hamburg, Germany
>> phone: +49-40-42838-7303 fax: +49-40-42838-7312
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>
>
>
-- 
Dr. Heike Pospisil
Center for Bioinformatics, University of Hamburg
Bundesstrasse 43, 20146 Hamburg, Germany
phone: +49-40-42838-7303 fax: +49-40-42838-7312