[BioC] Gene Selection

[Arne.Muller at sanofi-aventis.com]

Dear Heike,

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.

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

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?

Is that what you are looking for?

	kid regards,

	Arne

> -----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
> 
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