[BioC] Question

[Robert Gentleman]

On Thu, Jun 12, 2003 at 04:12:57PM +0200, Catherine.Eng at stud.unibas.ch wrote:
> HI,
> 
> I'm a student who begin to use R Language, I would like to know how to use 
> genefinder (in library genefilter) in order to search a pattern. In fact, is it 
> possible to assemble all values on the same rank.
> For example, I have 4 conditions and I search a specific profile. The problem 
> is the genes have differents intensities but they have close pattern of the 
> query.
> 
> ex: 3 genes A,B,C
>     4 conditons 
>     A(values): 30, 40, 50, 60 
>     B : 100, 110, 120, 130
>     C : 35, 50, 55, 65
> 

 You have to choose an appropriate distance metric (by default it is
 Euclidean) in this case you could either standardize across samples
 (be careful that this makes sense) or use a correlation base
 distances.

  Most of this stuff (including heatmaps,clustering and
  classification) depends on an appropriate metric

  Robert

> I search the gene with the same gene A profile, genefinder found gene C if I 
> limit numResults = 1.
> So, I would like to know if it's possible to superimpose on the gene A profile 
> and extract gene B. I played with genescale unsuccessful.
> 
> Can you help!
> 
> Thanks,
> 
>          Catherine   
> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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