[BioC] Gene Selection

[Heike Pospisil]

Dear Arne,

thanks for your reply.

>please correct me if I got it wrong: The experiment is a factorial design with factor 2 beeing nested within factor 1, i.e.
>
>1. the "category" with three levels (category 1 to 3)
>2. nested within within each level of the above factor there is another factor (sub-categories) with 3 to 4 levels.
>

That is exactly the design I have.

>What do you mean by "select differential expressed genes for one category"?
>

First, I want to select those genes discriminating between the 3 to 4 
sub-categories within one category. (e.g. "Which genes are significantly 
differentially expressed [up or down] for sub-category 'g' and not for 
all others?")

>I see two choices:
>
>1. is there an overall difference between the three main cateogies
>2. Within each category, are all sub-categories the same in terms of gene expression or is there a (any) difference?
>

The second question is that I am looking for.

Thanks for your help and best wishes,
Heike



>>-----Original Message-----
>>From: bioconductor-bounces at stat.math.ethz.ch
>>[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Heike
>>Pospisil
>>Sent: 04 February 2005 16:28
>>To: Naomi Altman
>>Cc: bioconductor at stat.math.ethz.ch
>>Subject: Re: [BioC] Gene Selection
>>
>>
>>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
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>    
>>
>
>
>  
>

-- 
Dr. Heike Pospisil
Center for Bioinformatics, University of Hamburg
Bundesstrasse 43, 20146 Hamburg, Germany
phone: +49-40-42838-7303 fax: +49-40-42838-7312