[BioC] Application of PAMR from Affy to spot data

[Robert Gentleman]

On Tue, Sep 28, 2004 at 01:04:00AM -0400, Tan, MinHan wrote:
> Good morning,
>  
> Sorry for the trouble.
> 
> I am trying to apply a pamr gene classifier obtained from Affymetrix
> data onto spot cDNA array data. For the Affy data, we have tumors , as
> well as several normals. The spot cDNA data is tumor against normal. 
>  
> I was hoping that I could get the small gene classifier, somehow (black
> box) modify this classifier with the mean value of the corresponding
> gene from normal tissue, and apply this with pamr.predict onto the spot
> data. 
>  
> I don't really know what Gaussian linear discrimination is, so I am a
> little lost in the original paper, but it seems that I should be
> modifying the discriminant scores somehow to construct estimates of the
> class probabilities.

  Hi,
   In general it doesn't make too much sense to develop a model based
   on one set of measurements (one type of measurements) on a
   different set of measurements. I would be quite skeptical of any
   results that did not involve some fairly rigorous description of
   why (and under what conditions) such a comparison would be
   sensible. 

   I believe that the first step should be deciding what comparisons
   between your two data sets (cDNA and Affy) are sensible, then you
   might try to find a model that captures those aspects of the data. 

   You might look at papers like Parmigiani et al, Clinical Cancer
   Research, 2004, or Choi et al, Bioinformatics, 2003. Both consider
   issues in combining or comparing microarray studies.

   Robert


>  
> I tried running pamr with all Affymetrix data converted to ratios.
> Results are definitely not as good as just using the rma expression
> values, which is my preferred option. 
>  
> I would appreciate any insights on this problem. Thank you!
> 
> Min-Han
> 
> This email message, including any attachments, is for the so...{{dropped}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

-- 
+---------------------------------------------------------------------------+
| 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        |
+---------------------------------------------------------------------------+